-
Notifications
You must be signed in to change notification settings - Fork 1
/
Makefile
705 lines (615 loc) · 53.2 KB
/
Makefile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
###### CHANGE THESE PATHS
ROOT=/lab/work/porchard/sn-muscle-project
HG19_FASTA=/lab/data/reference/human/hg19/hg19.fa
HG19_CHROM_SIZES=/lab/data/reference/human/hg19/hg19.chrom_sizes
HG19_BLACKLISTS=/lab/data/reference/human/hg19/annot/wgEncodeDacMapabilityConsensusExcludable.bed.gz /lab/data/reference/human/hg19/annot/wgEncodeDukeMapabilityRegionsExcludable.bed.gz
RN6_FASTA=/lab/work/porchard/data/fasta/rn6.fa
RN6_CHROM_SIZES=/lab/work/porchard/data/chrom_sizes/rn6.chrom_sizes
RN6_BLACKLISTS=/lab/work/porchard/data/mappability.new/rn6.blacklist.1.bed.gz
HG38_TO_HG19_CHAIN=/lab/work/porchard/data/chain/hg38ToHg19.over.chain.gz
#####
WORK=$(ROOT)/work
DATA=$(ROOT)/data
FIGURES=$(ROOT)/figures
SRC=$(ROOT)/src
BIN=$(ROOT)/bin
CONTROL=$(ROOT)/control
SAMPLE_INFO=$(ROOT)/sample_info/sample_info.txt
NAME = sn-muscle-project
CLUSTER_NAMES=$(ROOT)/2019-01-04-cluster-names.txt
SHARED_OPEN_CHROMATIN=$(WORK)/meuleman-with-hesc/results/common/common_open_chromatin.bed
PATH_TO_BULK=$(WORK)/bulk-atacseq/results
.PHONY: data sample_info all
ANALYSIS = $(WORK)/$@
CONFIG = $(ANALYSIS)/config.json
PIPELINE = $(ANALYSIS)/pipeline
##### https://stackoverflow.com/questions/7039811/how-do-i-process-extremely-long-lists-of-files-in-a-make-recipe
define NL
endef
#####
### SET UP DATA FILES ###
data: repeats liger-features dbSNP-vcf orthologues roadmap-posteriors ukb-summary-stats chromhmm other-annotations reformat-ukbb ldsc-baseline diamante-summary-stats manning-summary-stats gencode-coding gencode-bed meuleman-data meuleman encode-cisregulatory-elements encode-cres 1000G-SNPs motifs
cisbp-motifs: ANALYSIS=$(DATA)/$@
cisbp-motifs:
mkdir -p $(ANALYSIS)
cat /lab/work/porchard/snp-aware-pwm-scanning/data/TF_Information.txt | cut -f4,7 | awk '$$1!="."' | grep -v -w Motif_ID > $(ANALYSIS)/motif-id-to-tf-name.txt
gencode-tss-for-connections: ANALYSIS=$(DATA)/$@
gencode-tss-for-connections:
mkdir -p $(ANALYSIS)
cp /lab/data/reference/human/hg19/annot/gencode.v19.annotation.gtf.gz $(ANALYSIS)/
cd $(ANALYSIS) && python $(BIN)/gencodeGTFtoTSS.py gencode.v19.annotation.gtf.gz | sort | uniq | sort -k1,1 -k2n,2 > $(ANALYSIS)/hg19.bed
repeats: ANALYSIS=$(DATA)/$@
repeats:
mkdir -p $(ANALYSIS)
mysql --host=genome-mysql.cse.ucsc.edu --user=genome -D hg19 -e "SELECT * FROM simpleRepeat" > $(ANALYSIS)/trf_table.txt
cut -f2-4 $(ANALYSIS)/trf_table.txt | grep -v chromStart | sort -k1,1 -k2n,2 | bedtools merge -i stdin > $(ANALYSIS)/trf.bed
meuleman-data: ANALYSIS=$(DATA)/meuleman
meuleman-data:
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && wget https://www.meuleman.org/DHS_Index_and_Vocabulary_hg38_WM20190703.txt.gz
cd $(ANALYSIS) && wget https://www.meuleman.org/DHS_Index_and_Vocabulary_metadata.tsv
# DONE
meuleman-with-hesc:
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --dhs_index $(DATA)/meuleman/DHS_Index_and_Vocabulary_hg38_WM20190703.txt.gz --chain $(HG38_TO_HG19_CHAIN) --metadata $(DATA)/meuleman/DHS_Index_and_Vocabulary_metadata.tsv --dhs_matrix $(DATA)/meuleman/dat_bin_FDR01_hg38.RData $(ROOT)/prep-meuleman-with-hesc.nf &
# DONE
encode-cisregulatory-elements: ANALYSIS=$(DATA)/$@
encode-cisregulatory-elements:
cd $(ANALYSIS) && bash commands
encode-cres:
mkdir -p $(ANALYSIS)
echo "#!/bin/bash" > $(PIPELINE)
echo "#SBATCH --mem=10G" >> $(PIPELINE)
cd $(ANALYSIS) && echo "python $(ROOT)/bin/sort_uniq_gzip.py $(DATA)/encode-cisregulatory-elements/*.bed.gz | sort -k1,1 -k2n,2 > encode-cres.bed" >> $(PIPELINE) && sbatch $(PIPELINE)
gencode-coding: ANALYSIS=$(DATA)/$@
gencode-coding:
mkdir $(ANALYSIS) && cd $(ANALYSIS) && wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz && zcat gencode.v19.annotation.gtf.gz | awk '$$3=="CDS"' | cut -f1,4,5 | sort -k1,1 -k2n,2 -k3n,3 | bedtools merge -i stdin > coding.bed
gencode-bed: ANALYSIS=$(DATA)/$@
gencode-bed:
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gff3.gz && gunzip gencode.v19.annotation.gff3.gz
gff3ToGenePred $(ANALYSIS)/gencode.v19.annotation.gff3 $(ANALYSIS)/gencode.genePred
genePredToBed $(ANALYSIS)/gencode.genePred $(ANALYSIS)/gencode.hg19.bed
cd $(ANALYSIS) && wget ftp://ftp.ensembl.org/pub/release-101/gff3/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.101.gff3.gz && zcat Rattus_norvegicus.Rnor_6.0.101.gff3.gz > rn6.gff3
gff3ToGenePred -useName $(ANALYSIS)/rn6.gff3 $(ANALYSIS)/rn6.genePred
genePredToBed $(ANALYSIS)/rn6.genePred $(ANALYSIS)/rn6.bed
cat $(ANALYSIS)/rn6.bed | perl -pe 's/^/chr/' > $(ANALYSIS)/rn6.chromnames.bed
cd $(ANALYSIS) && python update-bed-to-gene-names.py gencode.v19.annotation.gff3 gencode.hg19.bed > gencode.hg19.genes.bed
motifs: ANALYSIS=$(DATA)/$@
motifs: MOTIFS=MEF2_known10 AP1_known5 PITX2_2
motifs:
mkdir -p $(ANALYSIS)
cp /lab/work/porchard/fimo/work/background/hg19.background.txt $(ANALYSIS)/
$(foreach m,$(MOTIFS),cp /lab/work/porchard/fimo/work/ENCODE2013/data/$(m).meme $(ANALYSIS)/$(NL))
$(foreach m,$(MOTIFS),meme2plain $(ANALYSIS)/$(m).meme | grep -v "^>" > $(ANALYSIS)/$(m).txt$(NL))
liger-features: ANALYSIS=$(DATA)/$@
liger-features:
# For each genome:
# get the GTF
# get the annotation report
# convert the chromosome names to ucsc style
# then, using python script:
# keep curated transcripts
# for each gene, merge all the transcripts, and keep 3 kb upstream (even if it overlaps with other stuff)
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Rattus_norvegicus/annotation_releases/current/GCF_000001895.5_Rnor_6.0/GCF_000001895.5_Rnor_6.0_assembly_report.txt && wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Rattus_norvegicus/annotation_releases/current/GCF_000001895.5_Rnor_6.0/GCF_000001895.5_Rnor_6.0_genomic.gtf.gz
cd $(ANALYSIS) && wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/105.20190906/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gtf.gz && wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/105.20190906/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_report.txt
python $(ROOT)/bin/refseq-annotation-and-report-to-feature-file.py $(ANALYSIS)/GCF_000001895.5_Rnor_6.0_genomic.gtf.gz $(ANALYSIS)/GCF_000001895.5_Rnor_6.0_assembly_report.txt | grep -v -e 'random' -e 'chrUn' | sort -k1,1 -k2n,2 -k3n,3 > $(ANALYSIS)/rn6.genes.bed
python $(ROOT)/bin/make-liger-features.py $(ANALYSIS)/rn6.genes.bed $(RN6_CHROM_SIZES) | sort -k1,1 -k2n,2 -k3n,3 > $(ANALYSIS)/rn6.features.bed
python $(ROOT)/bin/refseq-annotation-and-report-to-feature-file.py $(ANALYSIS)/GCF_000001405.25_GRCh37.p13_genomic.gtf.gz $(ANALYSIS)/GCF_000001405.25_GRCh37.p13_assembly_report.txt | grep -v -e 'random' -e 'chrUn' | sort -k1,1 -k2n,2 -k3n,3 > $(ANALYSIS)/hg19.genes.bed
python $(ROOT)/bin/make-liger-features.py $(ANALYSIS)/hg19.genes.bed $(HG19_CHROM_SIZES) | sort -k1,1 -k2n,2 -k3n,3 > $(ANALYSIS)/hg19.features.bed
# blacklist filter
bedtools intersect -a $(ANALYSIS)/rn6.features.bed -b $(RN6_BLACKLISTS) -v > $(ANALYSIS)/rn6.features.noblacklist
bedtools intersect -a $(ANALYSIS)/hg19.features.bed -b $(HG19_BLACKLISTS) -v > $(ANALYSIS)/hg19.features.noblacklist
diamante-summary-stats: ANALYSIS=$(DATA)/$@
diamante-summary-stats:
mkdir -p $(ANALYSIS)
ln -sf /lab/work/porchard/data/gwas/diamante/Mahajan.NatGenet2018b.T2D.European.txt $(ANALYSIS)/ # TODO: drop from final file
ln -sf /lab/work/porchard/data/gwas/diamante/Mahajan.NatGenet2018b.T2Dbmiadj.European.txt $(ANALYSIS)/ # TODO: drop from final file
cd $(ANALYSIS) && nohup python $(ROOT)/bin/prep-diamante-for-ldsc.py --vcf $(DATA)/dbSNP-vcf/All_20170710.vcf.gz $(ANALYSIS)/Mahajan.NatGenet2018b.T2D.European.txt diamante.T2D.European.ldsc.txt.gz &
cd $(ANALYSIS) && nohup python $(ROOT)/bin/prep-diamante-for-ldsc.py --vcf $(DATA)/dbSNP-vcf/All_20170710.vcf.gz $(ANALYSIS)/Mahajan.NatGenet2018b.T2Dbmiadj.European.txt diamante.T2Dbmiadj.European.ldsc.txt.gz &
manning-summary-stats: ANALYSIS=$(DATA)/$@
manning-summary-stats:
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && wget ftp://ftp.sanger.ac.uk/pub/magic/MAGIC_Manning_et_al_lnFastingInsulin_MainEffect.txt.gz && wget ftp://ftp.sanger.ac.uk/pub/magic/MAGIC_Manning_et_al_FastingGlucose_MainEffect.txt.gz
cd $(ANALYSIS) && Rscript $(ROOT)/bin/reformat-manning-summarystats-for-ldsc.R
ukb-summary-stats: ANALYSIS = $(DATA)/$@
ukb-summary-stats:
cd $(ANALYSIS) && wget -O ukb31063_h2_all.02Oct2019.tsv.gz https://www.dropbox.com/s/ipeqyhrpdqav5uh/ukb31063_h2_all.02Oct2019.tsv.gz?dl=1
cd $(ANALYSIS) && Rscript $(ROOT)/bin/choose-ukb-traits-new.R ukb31063_h2_all.02Oct2019.tsv.gz manifest.tsv && echo "# drmr:job" > wget-commands.sh && cut -f4 manifest-subset.tsv | perl -pe 's/.bgz$$/.gz/' >> wget-commands.sh && drmrarray -s 20 wget-commands.sh
ldsc-data: ANALYSIS=$(DATA)/$@
ldsc-data:
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && wget https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_baselineLD_v2.2_ldscores.tgz
cd $(ANALYSIS) && wget https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_frq.tgz && tar -xvzf 1000G_Phase3_frq.tgz
cd $(ANALYSIS) && wget https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_plinkfiles.tgz && tar -xvzf 1000G_Phase3_plinkfiles.tgz
cd $(ANALYSIS) && wget https://data.broadinstitute.org/alkesgroup/LDSCORE/hapmap3_snps.tgz && tar -xvzf hapmap3_snps.tgv
cd $(ANALYSIS) && wget https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_weights_hm3_no_MHC.tgz && tar -xvzf 1000G_Phase3_weights_hm3_no_MHC.tgz
cd $(ANALYSIS) && wget https://data.broadinstitute.org/alkesgroup/LDSCORE/w_hm3.snplist.bz2 && bzip2 -d w_hm3.snplist.bz2
cd $(ANALYSIS) && wget https://data.broadinstitute.org/alkesgroup/LDSCORE/weights_hm3_no_hla.tgz && tar -xvzf weights_hm3_no_hla.tgz
cd $(ROOT)/bin && python make-snp-id-conversions.py
ldsc-baseline-min-maf:
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && nohup nextflow run -resume -with-trace -with-report --results $(ANALYSIS)/results --projroot $(ROOT) $(ROOT)/ldsc-update-baseline-model-min-maf.nf &
chromhmm:
mkdir -p $(DATA)/$@
cd $(DATA)/$@ && wget https://zenodo.org/record/3524578/files/islet-cage-zenodo.tar.gz && tar -xvzf islet-cage-zenodo.tar.gz
cd $(DATA)/$@ && cp data/chromhmm/selected_annotated_states/files_by_state/* .
cd $(DATA)/$@ && rename 's/cell4_11.//' *
$(foreach t,Adipose SkeletalMuscle Liver Islets,cd $(DATA)/$@ && python $(BIN)/make-chromhmm-dense.py $(foreach s,Active_enhancer Active_TSS Bivalent_poised_TSS Flanking_TSS Genic_enhancer Quiescent_low_signal Repressed_polycomb Strong_transcription Weak_enhancer Weak_transcription Weak_TSS,$(t).$(s).bed) | sort -k1,1 -k2n,2 > $(t).dense.bed$(NL))
cd $(DATA)/$@ && rm -r data
other-annotations:
mkdir -p $(DATA)/$@
ln -s /lab/work/vivekrai/2019_mohlke_adipose/work/macs2/Adipose*.broadPeak $(DATA)/$@/
python $(ROOT)/bin/peak-sharing.py $(DATA)/$@/Adipose* | awk '$$4>=2' | cut -f1-3 | bedtools intersect -a stdin -b /lab/work/porchard/sn-muscle-project/data/mappability/hg19* -v > adipose.bed
cat /home/vivekrai/analyses/2018_NIH_Islets.snatacseq.v2/work/2019-03-01_clustering-final/peaks/1_peaks.broadPeak.noblacklist | cut -f1-3 | sort -k1,1 -k2n,2 > $(DATA)/$@/beta_ATAC.bed
cp /lab/work/vivekrai/2017_NIH_Islets.atacseq/work/2019-05-09_process-samples-subset/macs2/*.noblacklist $(DATA)/$@
cd $(DATA)/$@ && rm EndoC*
roadmap-posteriors:
cd $(DATA)/$@ && nohup bash $(ROOT)/src/download-roadmap-posteriors.sh &
reformat-ukbb:
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && nohup nextflow run -resume --projroot $(ROOT) -with-singularity $(ROOT)/singularity/general/general.simg --results $(ANALYSIS) $(ROOT)/reformat-ukbb.nf &
rnaseq:
mkdir -p $(ANALYSIS)
python $(CONTROL)/rnaseq/make_config.py $(ROOT) $(ROOT)/sample_info/sample_info.txt > $(CONFIG)
cd $(ANALYSIS) && nohup nextflow run -resume --chemistry V3 -with-trace -params-file $(CONFIG) -with-singularity /lab/work/porchard/singularity/archive/snRNA/2019-11-15/snRNA.simg -with-report -qs 300 --results $(ANALYSIS)/results /home/porchard/github/snRNAseq-NextFlow/main.nf &
rnaseq-dual-modality:
mkdir -p $(ANALYSIS)
ln -s /lab/work/porchard/Nova-315/work/rnaseq/results $(ANALYSIS)/
bulk-atacseq:
mkdir -p $(ANALYSIS)
python $(CONTROL)/$@/make_config.py $(ROOT) > $(ANALYSIS)/config.json
cd $(ANALYSIS) && nohup nextflow run -resume -with-singularity /lab/work/porchard/singularity/archive/ATAC/2019-11-20/ATAC.simg -with-dag -with-timeline -with-trace -with-report -params-file $(ANALYSIS)/config.json --results $(ANALYSIS)/results /home/porchard/github/ATACseq-NextFlow/main.nf &
atacseq:
mkdir -p $(ANALYSIS)
python $(CONTROL)/$@/make_config.py $(ROOT) $(ROOT)/sample_info/sample_info.with_facs.txt > $(CONFIG)
cp $(ROOT)/atac.nextflow.config $(ANALYSIS)/nextflow.config
cd $(ANALYSIS) && nohup nextflow run -resume -with-trace -params-file $(CONFIG) -with-singularity /lab/work/porchard/singularity/archive/snATAC/2019-11-07/snATAC.simg --low_read_count_threshold 1000 -with-report -qs 300 --results $(ANALYSIS)/results /home/porchard/github/snATACseq-NextFlow/main.nf &
atacseq-dual-modality:
mkdir -p $(ANALYSIS)
ln -s /lab/work/porchard/Nova-303/work/atacseq/results $(ANALYSIS)/
process-as-bulk:
mkdir -p $(ANALYSIS)/data/bams
cp $(WORK)/atacseq/results/merge/133* $(ANALYSIS)/data/bams/
cp $(WORK)/atacseq/results/merge/63_* $(ANALYSIS)/data/bams/
cp $(ROOT)/atac.nextflow.config $(ANALYSIS)/nextflow.config
cd $(ANALYSIS) && nohup nextflow run -resume --mapped_bam_glob '$(ANALYSIS)/data/bams/*.bam' -with-singularity $(ROOT)/singularity/ATAC.simg --results $(ANALYSIS)/results $(ROOT)/process-snATAC-as-bulk.nf &
counts-rna: ANALYSIS=$(WORK)/counts
counts-rna:
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --projroot $(ROOT) $(ROOT)/counts.nf &
fragment-counts-atac:
mkdir -p $(ANALYSIS)/data
ln -s $(WORK)/atacseq/results/prune/*.bam $(ANALYSIS)/data/
ln -s $(WORK)/atacseq-dual-modality/results/prune/*.bam $(ANALYSIS)/data/
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --projroot $(ROOT) --bam_glob '$(ANALYSIS)/data/*.bam' $(ROOT)/fragment-counts-atac.nf &
rnaseq-qc:
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --starsolo_dir_glob '$(WORK)/rnaseq/results/starsolo/*' $(ROOT)/make-rna-qc.nf &
qc:
mkdir -p $(ANALYSIS)
python $(ROOT)/control/$@/make_config.py $(ROOT) > $(ANALYSIS)/config.json
cd $(ANALYSIS) && nohup nextflow run -resume --rna_metrics '$(WORK)/rnaseq-qc/results/rnaseq-qc/*.txt' --initial_thresholds_rna $(ROOT)/initial-thresholds-rna.txt --initial_thresholds_atac $(ROOT)/initial-thresholds-atac.txt --library_labels $(ROOT)/library-labels.txt --results $(ANALYSIS)/results --genotypes $(DATA)/genotypes/genotypes.noblacklist.vcf.gz --demuxlet_mask $(WORK)/demuxlet-mask/demuxlet-mask.bed -params-file config.json $(ROOT)/$@.nf &
atac-correlation-fans: LIBRARIES=$(shell seq 133151 133154)
atac-correlation-fans: BULK_LIBRARIES=320-NM-1 320-NM-2
atac-correlation-fans:
mkdir -p $(ANALYSIS)/data/peaks
mkdir -p $(ANALYSIS)/data/bams
$(foreach l,$(LIBRARIES),ln -sf $(WORK)/process-as-bulk/results/prune/$(l)-hg19.pruned.bam $(ANALYSIS)/data/bams/$(NL))
$(foreach l,$(LIBRARIES),ln -sf $(WORK)/process-as-bulk/results/macs2/$(l)-hg19_peaks.broadPeak.noblacklist $(ANALYSIS)/data/peaks/$(NL))
$(foreach l,$(BULK_LIBRARIES),ln -sf $(PATH_TO_BULK)/macs2/$(l)_peaks.broadPeak.noblacklist $(ANALYSIS)/data/peaks/$(NL))
$(foreach l,$(BULK_LIBRARIES),ln -sf $(PATH_TO_BULK)/prune/$(l).pruned.bam $(ANALYSIS)/data/bams/$(NL))
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --bam_glob '$(ANALYSIS)/data/bams/*' --peak_glob '$(ANALYSIS)/data/peaks/*' $(ROOT)/atac-correlation.nf &
atac-correlation-loading: LIBRARIES=63_20 63_40
atac-correlation-loading: BULK_LIBRARIES=320-NM-1 320-NM-2 320-NM-3 320-NM-4
atac-correlation-loading:
mkdir -p $(ANALYSIS)/data/peaks
mkdir -p $(ANALYSIS)/data/bams
$(foreach l,$(LIBRARIES),ln -sf $(WORK)/process-as-bulk/results/prune/$(l)-hg19.pruned.bam $(ANALYSIS)/data/bams/$(NL))
$(foreach l,$(LIBRARIES),ln -sf $(WORK)/process-as-bulk/results/macs2/$(l)-hg19_peaks.broadPeak.noblacklist $(ANALYSIS)/data/peaks/$(NL))
$(foreach l,$(BULK_LIBRARIES),ln -sf $(PATH_TO_BULK)/macs2/$(l)_peaks.broadPeak.noblacklist $(ANALYSIS)/data/peaks/$(NL))
$(foreach l,$(BULK_LIBRARIES),ln -sf $(PATH_TO_BULK)/prune/$(l).pruned.bam $(ANALYSIS)/data/bams/$(NL))
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --bam_glob '$(ANALYSIS)/data/bams/*' --peak_glob '$(ANALYSIS)/data/peaks/*' $(ROOT)/atac-correlation.nf &
project-human-snps-to-rat:
mkdir -p $(ANALYSIS)
cat $(DATA)/diamante-credible-sets/genetic_credible_sets/* | grep -v Pos | cut -f2,3 | awk '{print($$1, $$2-20, $$2+20)}' | perl -pe 's/^/chr/; s/ /\t/g' > $(ANALYSIS)/snps-and-flanking.bed
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --bed_glob '$(ANALYSIS)/snps-and-flanking.bed' $(ROOT)/find-rat-snp.nf &
project-human-snps-to-rat-2:
mkdir -p $(ANALYSIS)
cat $(DATA)/diamante-credible-sets/genetic_credible_sets/* | grep -v Pos | cut -f2,3 | awk '{print($$1, $$2-1, $$2)}' | perl -pe 's/^/chr/; s/ /\t/g' > $(ANALYSIS)/snps-and-flanking.bed
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --bed_glob '$(ANALYSIS)/snps-and-flanking.bed' $(ROOT)/find-rat-snp.nf &
genotypes: ANALYSIS = $(DATA)/genotypes
genotypes:
mkdir -p $(ANALYSIS)
echo "7_KSm2 KSM2" > $(ANALYSIS)/rename.txt
echo "28_Ksm1 KSM1" >> $(ANALYSIS)/rename.txt
rm -rf rename-chroms.txt
$(foreach c,$(shell seq 1 22 | sort),echo '$(c) chr$(c)' >> rename-chroms.txt$(NL))
bcftools concat $(foreach c,$(shell seq 1 22 | sort),/lab/work/arushiv/muscle-sn/analyses/genotype_imputation/results/imputed_filtered_others/chr$(c).genotypes-rsid.vcf.gz) | bcftools view --samples 7_KSm2,28_Ksm1 | bcftools reheader --samples $(ANALYSIS)/rename.txt | bcftools annotate --rename-chrs rename-chroms.txt | bcftools view -o $(ANALYSIS)/genotypes.vcf.gz -Ob
rm -rf rename-chroms.txt
zcat $(DATA)/mappability/hg19.blacklist.* | sort -k1,1 -k2n,2 | bedtools merge > $(ANALYSIS)/blacklist.bed
bcftools view --targets-file ^$(ANALYSIS)/blacklist.bed -Ob -o $(ANALYSIS)/genotypes.noblacklist.vcf.gz $(ANALYSIS)/genotypes.vcf.gz
rm $(ANALYSIS)/blacklist.bed
diamante-locuszoom:
mkdir -p $(ANALYSIS)
printf "MarkerName\tP-value\n" > $(ANALYSIS)/gwas.txt
cat /lab/work/porchard/data/gwas/diamante/Mahajan.NatGenet2018b.T2D.European.txt | cut -f1,9 | grep -v Pvalue | perl -pe 's/^5:53271420\t/rs702634\t/; s/^12:26472562\t/rs7132434\t/' >> $(ANALYSIS)/gwas.txt
cd $(ANALYSIS) && locuszoom --metal $(ANALYSIS)/gwas.txt --refsnp rs702634 --flank 300kb --build hg19 --pop EUR --source 1000G_Nov2014 theme=publication height=6 hiStart=53269334 hiEnd=53278795
cd $(ANALYSIS) && locuszoom --metal $(ANALYSIS)/gwas.txt --refsnp rs7132434 --flank 300kb --build hg19 --pop EUR --source 1000G_Nov2014 theme=publication height=6 hiStart=26436640 hiEnd=26491955
diamante-bmiadj-locuszoom:
mkdir -p $(ANALYSIS)
printf "MarkerName\tP-value\n" > $(ANALYSIS)/gwas.txt
cat /lab/work/porchard/data/gwas/diamante/Mahajan.NatGenet2018b.T2Dbmiadj.European.txt | cut -f1,9 | grep -v Pvalue >> $(ANALYSIS)/gwas.txt
cd $(ANALYSIS) && locuszoom --metal $(ANALYSIS)/gwas.txt --refsnp 5:53271420 --flank 300kb --build hg19 --pop EUR --source 1000G_Nov2014 theme=publication height=6 hiStart=53269334 hiEnd=53278795
cd $(ANALYSIS) && locuszoom --metal $(ANALYSIS)/gwas.txt --refsnp 12:26472562 --flank 300kb --build hg19 --pop EUR --source 1000G_Nov2014 theme=publication height=6 hiStart=26436640 hiEnd=26491955
snp-overlap-with-encode-cres:
cat $(WORK)/encode-cres/encode-cres.bed | cut -f1-4 | uniq > $@.bed
bedtools closest -k 2 -d -a arl15-snp.bed -b $@.bed
bedtools closest -k 2 -d -a itpr2-snp.bed -b $@.bed
compare-to-liger:
mkdir -p $(ANALYSIS)/old-clustering
mkdir -p $(ANALYSIS)/new-clustering-1
cd $(ANALYSIS)/old-clustering && python $(BIN)/compare-to-old-clustering.py $(WORK)/downstream-new-features/results/liger/round-1/second-louvain-clusters.txt /lab/work/porchard/sn-muscle-project/work/process-by-cluster/clusters.txt $(ROOT)/library-labels.txt seurat-vs-old-liger 'LIGER cluster' 'Seurat cluster'
cat /lab/work/porchard/sn-muscle-project/work/liger-human-and-rat-with-lambda-10/results/post-factorization-3/KSM2_rat_RNA/10/clusters-10-0.04.txt | perl -pe 's/hg19[A-Z]*/hg19/; s/rn6[A-Z]*/rn6/; s/ /\t/g' > $(ANALYSIS)/clusters-no-dual-modality.txt; python $(BIN)/add-dual-modality-ATAC-to-clusters.py $(ANALYSIS)/clusters-no-dual-modality.txt > $(ANALYSIS)/clusters-new-liger.txt
cd $(ANALYSIS)/new-clustering-1 && python $(BIN)/compare-to-old-clustering.py $(ANALYSIS)/clusters-new-liger.txt /lab/work/porchard/sn-muscle-project/work/process-by-cluster/clusters.txt $(ROOT)/library-labels.txt seurat-vs-new-liger 'LIGER cluster' 'Seurat cluster'
tables:
mkdir -p $(ANALYSIS)/tables
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results $(ROOT)/make-tables.nf &
knit: ANALYSIS=$(ROOT)/knit
knit: all
# FANS vs no FANS figures
ln -sf $(WORK)/manuscript-figures-v2/results/fans-vs-no-fans/fans-chromhmm-overlap.pdf $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/fans-vs-no-fans/umis-vs-mitochondrial-fans-vs-no-fans.png $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/fans-vs-no-fans/fans-rna-correlation.png $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/fans-vs-no-fans/fans-gb.pdf $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/fans/fans-atac-correlation.png $(ANALYSIS)/
# 20k vs 40k figures
ln -sf $(WORK)/tables/results/figures/hqaa-vs-tss-enrich-loading.png $(ANALYSIS)/hqaa-vs-tss-enrichment-20k-vs-40k.png
ln -sf $(WORK)/tables/results/figures/hqaa-vs-max-frac-autosomal-loading.png $(ANALYSIS)/hqaa-vs-max-fraction-reads-from-single-autosome-20k-vs-40k.png
ln -sf $(WORK)/manuscript-figures-v2/results/20k-vs-40k/loading-chromhmm-overlap.pdf $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/20k-vs-40k/loading-gb.pdf $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/20k-vs-40k/umis-vs-mitochondrial-20k-vs-40k.png $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/20k-vs-40k/loading-rna-correlation.png $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/loading/loading-atac-correlation.png $(ANALYSIS)/
# dual modality QC figures
ln -sf $(WORK)/qc-plots-dual-modality/post-species-calling-qc.png $(ANALYSIS)/dual-modality-qc.png
ln -sf $(WORK)/qc-plots-dual-modality/human-vs-rat-atac-hqaa.png $(ANALYSIS)/dual-modality-human-vs-rat.png
ln -sf $(WORK)/determine-species-dual-modality/results/plot/*.png $(ANALYSIS)/
# Libraries used downstream
ln -sf $(WORK)/tables/results/figures/hqaa-vs-tss-enrich-all-used-downstream.png $(ANALYSIS)/hqaa-vs-tss-enrichment-used-downstream.png
ln -sf $(WORK)/tables/results/figures/hqaa-vs-max-frac-autosomal-all-used-downstream.png $(ANALYSIS)/hqaa-vs-max-fraction-reads-from-single-autosome-used-downstream.png
ln -sf $(WORK)/manuscript-figures-v2/results/qc-for-downstream-libraries/umis-vs-mitochondrial-used-downstream.png $(ANALYSIS)/
# clustering comparison
ln -sf $(WORK)/compare-to-liger/new-clustering-1/seurat-vs-new-liger.alluvial-new-to-old.png $(ANALYSIS)/seurat-vs-liger-alluvial.png
ln -sf $(WORK)/compare-to-liger/new-clustering-1/seurat-vs-new-liger.compare-to-old.png $(ANALYSIS)/seurat-vs-liger-heatmap.png
# Figures for the biology part of the manuscript
ln -sf $(WORK)/process-by-cluster/results/gene-expression-near-snps/chr12_26472562.png $(ANALYSIS)/gene-expression-near-ITPR2-locus.png
ln -sf $(WORK)/process-by-cluster/results/gene-expression-near-snps/chr5_53271420.png $(ANALYSIS)/gene-expression-near-ARL15-locus.png
ln -sf $(WORK)/process-by-cluster/results/figures/rubenstein-vs-our-fiber-type-lfcs.pdf $(ANALYSIS)/
ln -sf $(WORK)/process-by-cluster/results/figures/fiber-types-per-species-MYH7-vs-MYH1_2_4.png $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/compare-deltasvm-to-allelic-bias/dsvm-vs-allelic-bias-type-2-fibers-fdr-1-deltasvmZ-2-min-coverage-15.png $(ANALYSIS)/dsvm-vs-allelic-bias.png
ln -sf $(WORK)/manuscript-figures-v2/results/barcode-rank-plots/*.png $(ANALYSIS)/
ln -sf $(WORK)/chromvar/results/plot/*.png $(ANALYSIS)/
ln -sf $(WORK)/hic-overlap-gencode/results/figures/*.png $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/cicero-no-binarize-175Mb/chr5_53271420.png $(ANALYSIS)/ARL15-cicero.png
ln -sf $(WORK)/manuscript-figures-v2/results/cicero-no-binarize-175Mb/chr12_26472562.png $(ANALYSIS)/ITPR2-cicero.png
ln -sf $(WORK)/manuscript-figures-v2/results/seurat-links/spearman/chr12_26472562-peak-gene-links-heatmap.png $(ANALYSIS)/ITPR2-signac.png
ln -sf $(WORK)/manuscript-figures-v2/results/seurat-links/spearman/chr5_53271420-peak-gene-links-heatmap.png $(ANALYSIS)/ARL15-signac.png
$(foreach m,MEF2A MEF2B MEF2C MEF2D FOS JUN,ln -sf $(WORK)/process-by-cluster/results/figures/$(m).png $(ANALYSIS)/$(NL))
ln -sf $(WORK)/luciferase/luciferase-all.png $(ANALYSIS)/
ln -sf $(WORK)/diamante-deltaSVM/results/plot/5_53271420.png $(ANALYSIS)/
ln -sf $(WORK)/diamante-deltaSVM/results/plot/12_26453283.png $(ANALYSIS)/
ln -sf $(WORK)/ldsc/UKB-hesc/hg19/joint-model/results/heatmaps-and-tables/LDSC-UKB-across-all-cell-types.pdf $(ANALYSIS)/
ln -sf $(WORK)/ldsc/UKB-hesc/rn6/joint-model/results/heatmaps-and-tables/LDSC-UKB-across-all-cell-types.pdf $(ANALYSIS)/UKB-LDSC-by-rn6.pdf
# BMI unadjusted
ln -sf $(WORK)/manuscript-figures-v2/results/T2D-GWAS-enrichments-no-bmiadj/rn6/T2D-FIns.pdf $(ANALYSIS)/T2D-FIns-rn6.pdf
ln -sf $(WORK)/manuscript-figures-v2/results/gb-python/arl15-human-big.pdf $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/gb-python/itpr2-human-big.pdf $(ANALYSIS)/
ln -sf $(WORK)/manuscript-figures-v2/results/chromatin-state-legend/chrom_state_legend.pdf $(ANALYSIS)/
cd $(ANALYSIS) && pdflatex main.tex && pdflatex main.tex
diamante-credible-sets: ANALYSIS=$(DATA)/$@
diamante-credible-sets:
mkdir -p $(ANALYSIS)
cp -r /lab/data/gwas/2018_02_DIAMANTE/credible_sets/genetic_credible_sets $(ANALYSIS)/
hiC:
mkdir -p $(DATA)/$@
cd $(DATA)/$@ && wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87112/suppl/GSE87112_file.tar.gz
cd $(DATA)/$@ && tar -xvzf GSE87112_file.tar.gz && tar -xvzf FitHiC_primary_cohort.tgz
Rscript $(SRC)/format-hiC-data.R $(DATA)/$@/psoas-hic-connections.txt $(HG19_CHROM_SIZES) $(DATA)/$@/FitHiC_primary_cohort/FitHiC_output.PO_*
snatacseq-as-bulk:
mkdir -p $(ANALYSIS)
python $(CONTROL)/$@/make_config.py $(ROOT) $(ROOT)/sample_info/sample_info.with_facs.txt > $(ANALYSIS)/config.json
cd $(ANALYSIS) && nohup nextflow run -resume -with-singularity /lab/work/porchard/singularity/archive/ATAC/2019-11-20/ATAC.simg -with-dag -with-timeline -with-trace -with-report -params-file $(ANALYSIS)/config.json --results $(ANALYSIS)/results /home/porchard/github/ATACseq-NextFlow/main.nf &
dual-modality-quality-nuclei:
mkdir -p $(ANALYSIS)
cat /lab/work/porchard/daily/2020-11-18/labs/human-nuclei.tsv | grep -v rna_barcode | cut -f2 | perl -pe 's/^/1846_RNA-hg19\t/; s/$$/\tKSM2/' > $(ANALYSIS)/nuclei-with-individual-assignments.txt
cat /lab/work/porchard/daily/2020-11-18/labs/human-nuclei.tsv | grep -v rna_barcode | cut -f3 | perl -pe 's/^/1846_ATAC-hg19\t/; s/$$/\tKSM2/' >> $(ANALYSIS)/nuclei-with-individual-assignments.txt
cat /lab/work/porchard/daily/2020-11-18/labs/rat-nuclei.tsv | grep -v rna_barcode | cut -f2 | perl -pe 's/^/1846_RNA-rn6\t/; s/$$/\trat1/' >> $(ANALYSIS)/nuclei-with-individual-assignments.txt
cat /lab/work/porchard/daily/2020-11-18/labs/rat-nuclei.tsv | grep -v rna_barcode | cut -f3 | perl -pe 's/^/1846_ATAC-rn6\t/; s/$$/\trat1/' >> $(ANALYSIS)/nuclei-with-individual-assignments.txt
cat $(ANALYSIS)/nuclei-with-individual-assignments.txt | cut -f1-2 > $(ANALYSIS)/nuclei.txt
quality-nuclei-count-files:
mkdir -p $(ANALYSIS)/data/atac
mkdir -p $(ANALYSIS)/data/rna
cat $(WORK)/qc/results/call-nuclei-atac/pass-qc.tsv $(WORK)/qc/results/call-nuclei-rna/pass-qc.tsv $(WORK)/dual-modality-quality-nuclei/nuclei-with-individual-assignments.txt | sort | uniq > $(ANALYSIS)/data/nuclei-with-individual-assignments.txt
cut -f1-2 $(ANALYSIS)/data/nuclei-with-individual-assignments.txt > $(ANALYSIS)/data/nuclei.txt
ln -s $(WORK)/fragment-counts-atac/results/uncorrected-counts/*.counts.txt $(ANALYSIS)/data/atac/
ln -s $(WORK)/rnaseq/results/starsolo/* $(ANALYSIS)/data/rna
ln -s $(WORK)/rnaseq-dual-modality/results/starsolo/* $(ANALYSIS)/data/rna
# remove FANS atac libraries
rm $(ANALYSIS)/data/atac/133152-hg19*
rm $(ANALYSIS)/data/atac/133154-hg19*
cd $(ANALYSIS) && nohup nextflow run -resume --starsolo_dir_glob '$(ANALYSIS)/data/rna/*' --results $(ANALYSIS)/results --nuclei $(ANALYSIS)/data/nuclei.txt --atac_gene_count_glob '$(ANALYSIS)/data/atac/*' --individual_assignments $(ANALYSIS)/data/nuclei-with-individual-assignments.txt $(ROOT)/make-quality-nuclei-count-files.nf &
demuxlet-mask:
mkdir -p $(ANALYSIS)
python $(BIN)/make-demuxlet-mask.py --mask-top 0.3 $(WORK)/rnaseq/results/starsolo/63_40_rna-hg19/Solo.out/GeneFull/raw/features.tsv $(WORK)/rnaseq/results/starsolo/63_40_rna-hg19/Solo.out/GeneFull/raw/matrix.mtx /lab/data/reference/human/hg19/index/STAR/current/gencode.v19.annotation.gtf > $(ANALYSIS)/demuxlet-mask.bed
wasp-input-bams:
mkdir -p $(ANALYSIS)/data
cp $(WORK)/process-by-cluster/clusters.txt $(ANALYSIS)/data/clusters.txt
cat $(WORK)/quality-nuclei-count-files/data/nuclei-with-individual-assignments.txt | grep -v -w 133152-hg19 | grep -v -w 133154-hg19 > $(ANALYSIS)/data/nuclei-with-individual-assignments.txt
ln -s $(WORK)/atacseq/results/merge/*.bam $(ANALYSIS)/data/
ln -s $(WORK)/atacseq-dual-modality/results/merge/*.bam $(ANALYSIS)/data/
# delete the FANS atac libraries
rm -rf $(ANALYSIS)/data/133152-hg19*
rm -rf $(ANALYSIS)/data/133154-hg19*
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --bam_glob '$(ANALYSIS)/data/*.bam' --clusters $(ANALYSIS)/data/clusters.txt --nuclei_with_individual_assignments $(ANALYSIS)/data/nuclei-with-individual-assignments.txt $(ROOT)/make-wasp-input-bams.nf &
atac-allelic-bias-by-cell-type:
mkdir -p $(ANALYSIS)/data
ln -s $(WORK)/wasp-input-bams/results/split-library-by-individual-and-cluster/*hg19*.bam $(ANALYSIS)/data/
cd $(ANALYSIS) && nohup nextflow run -resume --vcf $(DATA)/genotypes/genotypes.noblacklist.vcf.gz --results $(ANALYSIS)/results --bam_glob '$(ANALYSIS)/data/*.bam' $(ROOT)/atac-allelic-bias-by-cell-type.nf &
seurat-joint-2:
mkdir -p $(ANALYSIS)/data
ln -s $(WORK)/quality-nuclei-count-files/results/liger-in/* $(ANALYSIS)/data/
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --liger_in '$(ANALYSIS)/data/*' $(ROOT)/seurat-2.nf &
liger-human-and-rat-with-lambda-10:
mkdir -p $(ANALYSIS)/data
ln -s $(WORK)/quality-nuclei-count-files/results/liger-in/* $(ANALYSIS)/data/
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --liger_in '$(ANALYSIS)/data/*' --lambda 10 $(ROOT)/liger-human-and-rat-with-lambda.nf &
process-by-cluster:
mkdir -p $(ANALYSIS)/data
ln -s $(WORK)/atacseq/results/prune/*.bam $(ANALYSIS)/data/
ln -s $(WORK)/atacseq-dual-modality/results/prune/*.bam $(ANALYSIS)/data/
# remove FANS atac libraries
rm $(ANALYSIS)/data/133152-hg19*
rm $(ANALYSIS)/data/133154-hg19*
python $(CONTROL)/process-by-cluster/make_config.py $(ANALYSIS)/data/*.bam > $(CONFIG)
cp /lab/work/porchard/sn-muscle-project/work/seurat-joint-2/results/seurat-out/seurat-clusters.txt $(ANALYSIS)/clusters-no-dual-modality.txt
python $(BIN)/add-dual-modality-ATAC-to-clusters.py $(ANALYSIS)/clusters-no-dual-modality.txt > $(ANALYSIS)/clusters.txt
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results -params-file $(CONFIG) --library_labels $(ROOT)/library-labels.txt --liger_in_matrices_glob '$(WORK)/liger-human-and-rat-with-lambda-5/data/*' --cluster_names $(ROOT)/cluster-names.txt --clusters $(ANALYSIS)/clusters.txt $(ROOT)/process-by-cluster.nf &
### GWAS ENRICHMENTS ###
ldsc-T2D-one-model-per-cluster-hg19: ANALYSIS=$(WORK)/ldsc/T2D/hg19/one-model-per-cluster
ldsc-T2D-one-model-per-cluster-hg19:
mkdir -p $(ANALYSIS)/data
$(foreach c,$(shell seq 0 6),cat $(WORK)/process-by-cluster/results/peaks/broad/$(c)-hg19_peaks.broadPeak.noblacklist | sort -k1,1 -k2n,2 | cut -f1-3 > $(ANALYSIS)/data/cluster_$(c).bed$(NL))
cp $(DATA)/other-annotations/beta_ATAC.bed $(ANALYSIS)/data/beta_cell.bed
cp $(DATA)/other-annotations/adipose.bed $(ANALYSIS)/data/adipose.bed
cp $(WORK)/meuleman-with-hesc/results/tissues/Liver.bed $(ANALYSIS)/data/liver.bed
cd $(ANALYSIS) && nohup nextflow run -resume -with-trace -with-report --other_annotations '$(SHARED_OPEN_CHROMATIN)' --projroot $(ROOT) --results $(ANALYSIS)/results --cluster_names $(CLUSTER_NAMES) $(ROOT)/ldsc-T2D-one-model-per-cell-type.nf --peak_glob '$(ANALYSIS)/data/*.bed' &
ldsc-T2D-one-model-per-cluster-rn6: ANALYSIS=$(WORK)/ldsc/T2D/rn6/one-model-per-cluster
ldsc-T2D-one-model-per-cluster-rn6:
mkdir -p $(ANALYSIS)/data
$(foreach c,$(shell seq 0 6),cat $(WORK)/process-by-cluster/results/rat-peak-liftover/$(c)-rn6_peaks_in_hg19.bed | sort -k1,1 -k2n,2 | cut -f1-3 > $(ANALYSIS)/data/cluster_$(c).bed$(NL))
cp $(DATA)/other-annotations/beta_ATAC.bed $(ANALYSIS)/data/beta_cell.bed
cp $(DATA)/other-annotations/adipose.bed $(ANALYSIS)/data/adipose.bed
cp $(WORK)/meuleman-with-hesc/results/tissues/Liver.bed $(ANALYSIS)/data/liver.bed
cd $(ANALYSIS) && nohup nextflow run -resume -with-trace -with-report --other_annotations '$(SHARED_OPEN_CHROMATIN)' --projroot $(ROOT) --results $(ANALYSIS)/results --cluster_names $(CLUSTER_NAMES) $(ROOT)/ldsc-T2D-one-model-per-cell-type.nf --peak_glob '$(ANALYSIS)/data/*.bed' &
ldsc-T2D-joint-model-hg19: ANALYSIS=$(WORK)/ldsc/T2D/hg19/joint-model
ldsc-T2D-joint-model-hg19:
mkdir -p $(ANALYSIS)/data
$(foreach c,$(shell seq 0 6),cat $(WORK)/process-by-cluster/results/peaks/broad/$(c)-hg19_peaks.broadPeak.noblacklist | sort -k1,1 -k2n,2 | cut -f1-3 > $(ANALYSIS)/data/cluster_$(c).bed$(NL))
cp $(DATA)/other-annotations/beta_ATAC.bed $(ANALYSIS)/data/beta_cell.bed
cp $(DATA)/other-annotations/adipose.bed $(ANALYSIS)/data/adipose.bed
cp $(WORK)/meuleman-with-hesc/results/tissues/Liver.bed $(ANALYSIS)/data/liver.bed
cd $(ANALYSIS) && nohup nextflow run -resume -with-trace -with-report --other_annotations '$(SHARED_OPEN_CHROMATIN)' --projroot $(ROOT) --results $(ANALYSIS)/results --cluster_names $(CLUSTER_NAMES) $(ROOT)/ldsc-T2D-joint-model.nf --peak_glob '$(ANALYSIS)/data/*.bed' &
ldsc-T2D-joint-model-rn6: ANALYSIS=$(WORK)/ldsc/T2D/rn6/joint-model
ldsc-T2D-joint-model-rn6:
mkdir -p $(ANALYSIS)/data
$(foreach c,$(shell seq 0 6),cat $(WORK)/process-by-cluster/results/rat-peak-liftover/$(c)-rn6_peaks_in_hg19.bed | sort -k1,1 -k2n,2 | cut -f1-3 > $(ANALYSIS)/data/cluster_$(c).bed$(NL))
cp $(DATA)/other-annotations/beta_ATAC.bed $(ANALYSIS)/data/beta_cell.bed
cp $(DATA)/other-annotations/adipose.bed $(ANALYSIS)/data/adipose.bed
cp $(WORK)/meuleman-with-hesc/results/tissues/Liver.bed $(ANALYSIS)/data/liver.bed
cd $(ANALYSIS) && nohup nextflow run -resume -with-trace -with-report --other_annotations '$(SHARED_OPEN_CHROMATIN)' --projroot $(ROOT) --results $(ANALYSIS)/results --cluster_names $(CLUSTER_NAMES) $(ROOT)/ldsc-T2D-joint-model.nf --peak_glob '$(ANALYSIS)/data/*.bed' &
ldsc-ukb-hg19-hesc: OTHER_ANNOTATIONS = $(shell ls $(WORK)/meuleman-with-hesc/results/tissues/*.bed) $(shell ls $(DATA)/other-annotations/*.bed)
ldsc-ukb-hg19-hesc: ANALYSIS=$(WORK)/ldsc/UKB-hesc/hg19/joint-model
ldsc-ukb-hg19-hesc:
mkdir -p $(ANALYSIS)/data
$(foreach f,$(OTHER_ANNOTATIONS),#cp $(f) $(ANALYSIS)/data/$(NL))
$(foreach c,$(shell seq 0 6),#cp $(WORK)/process-by-cluster/results/peaks/broad/$(c)-hg19_peaks.broadPeak.noblacklist $(ANALYSIS)/data/cluster_$(c).bed$(NL))
#cd $(ANALYSIS)/data && rm -rf Amion.bed Esophagus.bed Periodontal_Ligament.bed
cd $(ANALYSIS) && nohup nextflow run -resume -with-trace -with-report --projroot $(ROOT) --results $(ANALYSIS)/results $(ROOT)/ldsc-UKB-new-baseline.nf --other_annotations '$(SHARED_OPEN_CHROMATIN)' --trait_list $(ROOT)/ukb-traits.txt --peak_glob '$(ANALYSIS)/data/*.bed' &
ldsc-ukb-rn6-hesc: OTHER_ANNOTATIONS = $(shell ls $(WORK)/meuleman-with-hesc/results/tissues/*.bed) $(shell ls $(DATA)/other-annotations/*.bed)
ldsc-ukb-rn6-hesc: ANALYSIS=$(WORK)/ldsc/UKB-hesc/rn6/joint-model
ldsc-ukb-rn6-hesc:
mkdir -p $(ANALYSIS)/data
$(foreach f,$(OTHER_ANNOTATIONS),#cp $(f) $(ANALYSIS)/data/$(NL))
$(foreach c,$(shell seq 0 6),#cp $(WORK)/process-by-cluster/results/rat-peak-liftover/$(c)-rn6_peaks_in_hg19.bed $(ANALYSIS)/data/cluster_$(c).bed$(NL))
#cd $(ANALYSIS)/data && rm -rf Amion.bed Esophagus.bed Periodontal_Ligament.bed
cd $(ANALYSIS) && nohup nextflow run -resume -with-trace -with-report --projroot $(ROOT) --results $(ANALYSIS)/results $(ROOT)/ldsc-UKB-new-baseline.nf --other_annotations '$(SHARED_OPEN_CHROMATIN)' --trait_list $(ROOT)/ukb-traits.txt --peak_glob '$(ANALYSIS)/data/*.bed' &
find-peak-gene-links-across-clusters-2:
mkdir -p $(ANALYSIS)
cat $(WORK)/process-by-cluster/results/master-peak-counts/1846_ATAC-hg19.*.counts.txt > $(ANALYSIS)/counts.txt
cat $(ANALYSIS)/counts.txt | cut -f3 | perl -pe 's/:/\t/g' > $(ANALYSIS)/peaks.txt
cat $(ANALYSIS)/counts.txt | cut -f2,4 > $(ANALYSIS)/barcodes.txt
paste $(ANALYSIS)/peaks.txt $(ANALYSIS)/barcodes.txt > $(ANALYSIS)/counts.txt
cut -f4 $(ANALYSIS)/counts.txt | uniq | sort | uniq > $(ANALYSIS)/include-barcodes.txt
python $(BIN)/atac-peak-counts-to-hdf5.py $(ANALYSIS)/counts.txt $(ANALYSIS)/include-barcodes.txt $(ANALYSIS)/atac_counts.hdf5
cp $(WORK)/quality-nuclei-count-files/results/rna-corrected/1846_RNA-hg19.hdf5 $(ANALYSIS)/rna_counts.hdf5
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --clusters $(WORK)/process-by-cluster/clusters.txt --atac $(ANALYSIS)/atac_counts.hdf5 --rna $(ANALYSIS)/rna_counts.hdf5 $(ROOT)/signac-link-peaks-to-genes-across-clusters-flexible.nf &
manuscript-figures-v2:
mkdir -p $(ANALYSIS)/data/other-tissues
mkdir -p $(ANALYSIS)/data/human-muscle
mkdir -p $(ANALYSIS)/data/rat-muscle
ln -sf $(WORK)/browser-sessions/2020-sn-muscle-GWAS-overlap/results/bigwigs/* $(ANALYSIS)/data/other-tissues/
ln -sf $(WORK)/process-by-cluster/results/bigwigs/atac/*hg19* $(ANALYSIS)/data/human-muscle/
ln -sf $(WORK)/process-by-cluster/results/bigwigs/atac/*rn6* $(ANALYSIS)/data/rat-muscle/
rm $(ANALYSIS)/data/other-tissues/liver*
rm $(ANALYSIS)/data/human-muscle/all*
rm $(ANALYSIS)/data/rat-muscle/all*
cd $(ANALYSIS) && nohup nextflow run --rat_muscle_bw_glob '$(ANALYSIS)/data/rat-muscle/*' --human_muscle_bw_glob '$(ANALYSIS)/data/human-muscle/*' --other_bw_glob '$(ANALYSIS)/data/other-tissues/*' -resume --results $(ANALYSIS)/results --projroot $(ROOT) $(ROOT)/manuscript-figures-v2.nf &
delta-svm: NUMBER_PEAKS_KEEP=40000
delta-svm: FASTA=$(HG19_FASTA)
delta-svm: CHROM_SIZES=$(HG19_CHROM_SIZES)
delta-svm: GENOME=hg19
delta-svm: BLACKLISTS=$(HG19_BLACKLISTS)
delta-svm: SNP_FILE=/lab/work/porchard/sn-muscle-project/work/1000G-SNP-vcf/1000G-snps.vcf.gz
delta-svm: ANALYSIS=$(WORK)/delta-svm/all-keep-40k
delta-svm:
mkdir -p $(ANALYSIS)/data
$(foreach c,$(shell seq 0 6),cat $(WORK)/process-by-cluster/results/peaks/narrow/$(c)-$(GENOME)_peaks.narrowPeak.noblacklist | sort -k9n,9 | tail -n $(NUMBER_PEAKS_KEEP) > $(ANALYSIS)/data/cluster_$(c).narrow.bed$(NL))
$(foreach c,$(shell seq 0 6),cp $(WORK)/process-by-cluster/results/peaks/broad/$(c)-$(GENOME)_peaks.broadPeak.noblacklist $(ANALYSIS)/data/cluster_$(c).broad.bed$(NL))
cd $(ANALYSIS) && cp $(ROOT)/deltasvm-config.nf nextflow.config && NXF_VER=19.10.0 nohup ~/github/snATAC_deltaSVM/main.nf -resume --repeat_bed $(DATA)/repeats/trf.bed --max_repeat_content 0.6 --results_dir $(ANALYSIS)/results --kernel 2 --peak_dir '$(ANALYSIS)/data/cluster_*.narrow.bed' --broadpeak_dir '$(ANALYSIS)/data/cluster_*.broad.bed' --exclude '$(BLACKLISTS)' --ref $(FASTA) --human_ref $(HG19_FASTA) --snp_file $(SNP_FILE) --chrom_sizes $(CHROM_SIZES) --workDir $(ANALYSIS)/work &
gkmexplain:
mkdir -p $(ANALYSIS)/data
$(foreach c,$(shell seq 0 6),cp $(WORK)/delta-svm/all-keep-40k/results/cluster_$(c)/model.model.txt $(ANALYSIS)/data/cluster_$(c).model.txt$(NL))
cd $(ANALYSIS) && nohup nextflow run -resume --meme_glob '$(DATA)/motifs/*.meme' --fimo_background $(DATA)/motifs/hg19.background.txt --plain_motif_glob '$(DATA)/motifs/*.txt' --snp_file $(ROOT)/snps-for-manuscript.txt --results $(ANALYSIS)/results --model_glob '$(ANALYSIS)/data/*' $(ROOT)/gkmexplain-and-fimo-new-plots.nf &
find-disrupted-motifs:
mkdir -p $(ANALYSIS)/data/motifs
cp /lab/work/porchard/fimo/work/ENCODE2013/data/*.meme $(ANALYSIS)/data/motifs/
rm $(ANALYSIS)/data/motifs/*_disc*
cd $(ANALYSIS) && nohup nextflow run -resume --meme_glob '$(ANALYSIS)/data/motifs/*.meme' --fimo_background $(DATA)/motifs/hg19.background.txt --snp_file $(ROOT)/snps-for-manuscript.txt --results $(ANALYSIS)/results $(ROOT)/find-disrupted-motifs.nf &
get-deltasvm-z-scores:
mkdir -p $(ANALYSIS)
cat snps-for-manuscript.txt | perl -pe 's/ /\t/g' | cut -f1,2 | grep -v BP | perl -pe 's/^/chr/' > $(ANALYSIS)/pos-file.txt
$(foreach c,$(shell seq 0 6),python $(ROOT)/bin/get-deltaSVM-z-scores.py --deltaSVM-file $(WORK)/delta-svm/all-keep-40k/results/cluster_$(c)/snp_scores_cluster_$(c).txt --pos-file $(ANALYSIS)/pos-file.txt > $(ANALYSIS)/cluster_$(c).z-scores.txt$(NL))
logistic-regression-hg19: ANALYSIS=$(WORK)/logistic-regression/hg19
logistic-regression-hg19:
mkdir -p $(ANALYSIS)/data
cp $(WORK)/process-by-cluster/results/peaks/broad/*hg19*_peaks.broadPeak.noblacklist $(ANALYSIS)/data
rm $(ANALYSIS)/data/all*
cd $(ANALYSIS) && nohup nextflow run -resume -with-trace -with-report --results $(ANALYSIS)/results --broadpeak_glob '$(ANALYSIS)/data/*' --genome hg19 --projroot $(ROOT) $(ROOT)/logistic-regression.nf &
logistic-regression-rn6: ANALYSIS=$(WORK)/logistic-regression/rn6
logistic-regression-rn6:
mkdir -p $(ANALYSIS)/data
cp $(WORK)/process-by-cluster/results/peaks/broad/*rn6*_peaks.broadPeak.noblacklist $(ANALYSIS)/data
rm $(ANALYSIS)/data/all*
cd $(ANALYSIS) && nohup nextflow run -resume -with-trace -with-report --results $(ANALYSIS)/results --broadpeak_glob '$(ANALYSIS)/data/*' --genome rn6 --projroot $(ROOT) $(ROOT)/logistic-regression.nf &
chromvar:
mkdir -p $(ANALYSIS)/data/motifs
mkdir -p $(ANALYSIS)/data/peaks
mkdir -p $(ANALYSIS)/data/bams
ln -s /lab/work/porchard/fimo/work/cisBP/* $(ANALYSIS)/data/motifs/
ln -s $(WORK)/process-by-cluster/results/aggregate-of-quality-nuclei/bam/*hg19.bam $(ANALYSIS)/data/bams/
cp $(WORK)/process-by-cluster/results/peaks/broad/*hg19_peaks.broadPeak.noblacklist $(ANALYSIS)/data/peaks/
rm $(ANALYSIS)/data/peaks/all*
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --motif_to_tf $(DATA)/cisbp-motifs/motif-id-to-tf-name.txt --cluster_names $(ROOT)/cluster-names.txt --clusters $(WORK)/process-by-cluster/clusters.txt --fimo_glob '$(ANALYSIS)/data/motifs/*' --bam_glob '$(ANALYSIS)/data/bams/*' --peak_glob '$(ANALYSIS)/data/peaks/*' $(ROOT)/$@.nf &
luciferase:
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && python $(BIN)/luciferase.py > out.txt
cicero-no-binarize:
mkdir -p $(ANALYSIS)/data
ln -s $(WORK)/process-by-cluster/results/peak-counts/* $(ANALYSIS)/data/
zcat /home/porchard/github/ataqv/data/tss/hg19.tss.refseq.bed.gz | grep -v 'hap' > $(ANALYSIS)/hg19.tss.bed
python $(BIN)/add-dual-modality-ATAC-to-umap.py $(WORK)/seurat-joint-2/results/seurat-out/seurat-umap.txt | perl -pe 's/\t/-/' > $(ANALYSIS)/data/umap.txt
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --tss $(ANALYSIS)/hg19.tss.bed --counts_glob '$(ANALYSIS)/data/*.counts.txt' --snps $(ROOT)/cicero-snps.bed --umap $(ANALYSIS)/data/umap.txt $(ROOT)/cicero-no-binarize.nf &
diamante-deltaSVM:
mkdir -p $(ANALYSIS)/data
cp /lab/work/porchard/sn-muscle-project/work/process-by-cluster/results/peaks/broad/*hg19_peaks.broadPeak.noblacklist $(ANALYSIS)/data
rm $(ANALYSIS)/data/all*
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --peak_file_glob '$(ANALYSIS)/data/*' --cs_file_glob '$(DATA)/diamante-credible-sets/genetic_credible_sets/*' --dsvm_file_glob '$(WORK)/delta-svm/all-keep-40k/results/cluster_*/snp_scores_cluster_*.txt' $(ROOT)/delta-svm-diamante-loci.nf &
hic-overlap-gencode:
mkdir -p $(ANALYSIS)
bedtools intersect -wa -b arl15-snp.bed -a work/process-by-cluster/results/process-by-cluster-round-1/master-peaks/master-peaks.hg19.bed | perl -pe 's/$$/\tARL15_peak/'> $(ANALYSIS)/peaks.bed
bedtools intersect -wa -b itpr2-snp.bed -a work/process-by-cluster/results/process-by-cluster-round-1/master-peaks/master-peaks.hg19.bed | perl -pe 's/$$/\tITPR2_peak/' >> $(ANALYSIS)/peaks.bed
cp /lab/work/porchard/sn-muscle-project/data/gencode-tss-for-connections/hg19.bed $(ANALYSIS)/hg19.tss.bed
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --pchic_glob '$(DATA)/pc-hiC/po-*.xlsx' --yue_glob '$(DATA)/hic-yue-lab/hg19/*' --peaks $(ANALYSIS)/peaks.bed --fithic_glob '$(DATA)/hiC/FitHiC_primary_cohort/*' --bins $(DATA)/hiC/bins.bed --snp_bed $(ROOT)/cicero-snps.bed --tss $(ANALYSIS)/hg19.tss.bed $(ROOT)/hic.nf &
qc-plots-dual-modality:
mkdir -p $(ANALYSIS)
cd $(ANALYSIS) && python $(BIN)/sn-dual-modality-qc.py
plot-rna-and-atac-rat-human-mixing:
mkdir -p $(ANALYSIS)
grep 1846_ATAC-rn6 $(WORK)/process-by-cluster/clusters.txt | shuf | head -n 5 | cut -f2 > $(ANALYSIS)/barcodes.txt
grep 1846_ATAC-hg19 $(WORK)/process-by-cluster/clusters.txt | shuf | head -n 5 | cut -f2 >> $(ANALYSIS)/barcodes.txt
python $(BIN)/filter-bam-by-barcode.py $(WORK)/atacseq-dual-modality/results/mark_duplicates/1846_ATAC-hg19.md.bam $(ANALYSIS)/hg19-atac.bam $(ANALYSIS)/barcodes.txt
python $(BIN)/filter-bam-by-barcode.py $(WORK)/atacseq-dual-modality/results/mark_duplicates/1846_ATAC-rn6.md.bam $(ANALYSIS)/rn6-atac.bam $(ANALYSIS)/barcodes.txt
samtools index $(ANALYSIS)/hg19-atac.bam
samtools index $(ANALYSIS)/rn6-atac.bam
cd $(ANALYSIS) && python $(BIN)/count-species-unique-mapping-atac.py ~/github/snATACseq-NextFlow/737K-arc-v1.txt $(WORK)/atacseq-dual-modality/results/mark_duplicates/1846_ATAC-hg19.md.bam $(WORK)/atacseq-dual-modality/results/mark_duplicates/1846_ATAC-rn6.md.bam hg19 rn6 > $(ANALYSIS)/1846_ATAC.txt
cd $(ANALYSIS) && python $(BIN)/count-species-unique-mapping-atac.py ~/github/snATACseq-NextFlow/737K-arc-v1.txt $(ANALYSIS)/hg19-atac.bam $(ANALYSIS)/rn6-atac.bam hg19 rn6 > $(ANALYSIS)/1846_ATAC.txt
determine-species-dual-modality:
mkdir -p $(ANALYSIS)/data
ln -s $(WORK)/atacseq-dual-modality/results/mark_duplicates/1846_ATAC-hg19.md.bam $(ANALYSIS)/data/1846_ATAC-hg19.bam
ln -s $(WORK)/atacseq-dual-modality/results/mark_duplicates/1846_ATAC-rn6.md.bam $(ANALYSIS)/data/1846_ATAC-rn6.bam
ln -s $(WORK)/rnaseq-dual-modality/results/starsolo/1846_RNA-hg19/Aligned.sortedByCoord.out.bam $(ANALYSIS)/data/1846_RNA-hg19.bam
ln -s $(WORK)/rnaseq-dual-modality/results/starsolo/1846_RNA-rn6/Aligned.sortedByCoord.out.bam $(ANALYSIS)/data/1846_RNA-rn6.bam
cd $(ANALYSIS) && nohup nextflow run -resume --results $(ANALYSIS)/results --atac_glob '$(ANALYSIS)/data/*ATAC*' --rna_glob '$(ANALYSIS)/data/*RNA*' --rna_whitelist ~/github/snRNAseq-NextFlow/737K-arc-v1.txt --atac_whitelist ~/github/snATACseq-NextFlow/737K-arc-v1.txt $(ROOT)/$@.nf &
test-droplet-utils: SOLO_DIR=/lab/work/porchard/Nova-315/work/rnaseq-chimeric/results/starsolo/1846_RNA-hg19_rn6/Solo.out
test-droplet-utils:
mkdir -p $(ANALYSIS)
cat $(SOLO_DIR)/GeneFull/raw/features.tsv | perl -pe 's/$$/\tGene Expression/' > $(ANALYSIS)/features.tsv
cp $(SOLO_DIR)/GeneFull/raw/matrix.mtx $(ANALYSIS)/matrix.mtx
cp $(SOLO_DIR)/GeneFull/raw/barcodes.tsv $(ANALYSIS)/barcodes.tsv
cd $(ANALYSIS) && gzip *.tsv *.mtx
cd $(ANALYSIS) && Rscript $(BIN)/droplet-utils.R $(ANALYSIS)/ 1846_RNA
make-read-beds:
mkdir -p $(ANALYSIS)/data/atac
mkdir -p $(ANALYSIS)/data/rna
ln -s /lab/work/porchard/sn-muscle-project/work/atacseq/results/prune/*pruned.bam $(ANALYSIS)/data/atac/
ln -s /lab/work/porchard/sn-muscle-project/work/rnaseq/results/prune/*before-dedup.bam $(ANALYSIS)/data/rna/
ln -s /lab/work/porchard/sn-muscle-project/work/atacseq-dual-modality/results/prune/*pruned.bam $(ANALYSIS)/data/atac/
ln -s /lab/work/porchard/sn-muscle-project/work/rnaseq-dual-modality/results/prune/*before-dedup.bam $(ANALYSIS)/data/rna/
$(foreach r,1 2 3 4,ln -s $(WORK)/bulk-atacseq/results/prune/320-NM-$(r).pruned.bam $(ANALYSIS)/data/atac/$(NL))
cd $(ANALYSIS) && nohup nextflow run -resume --rna_bam_glob '$(ANALYSIS)/data/rna/*.bam' --atac_bam_glob '$(ANALYSIS)/data/atac/*.bam' --results $(ANALYSIS)/results $(ROOT)/$@.nf &
starch-bdg:
mkdir -p $(ANALYSIS)/data
cp $(WORK)/process-by-cluster/results/peaks/broad/*treat_pileup.bdg $(ANALYSIS)/data/
rm -rf $(ANALYSIS)/data/all*
cp $(WORK)/bulk-atacseq/results/macs2/*treat_pileup.bdg $(ANALYSIS)/data/
cp $(WORK)/process-as-bulk/results/macs2/*treat_pileup.bdg $(ANALYSIS)/data/
cd $(ANALYSIS) && nohup nextflow run -resume --bdg_glob '$(ANALYSIS)/data/*.bdg' --results $(ANALYSIS)/results $(ROOT)/$@.nf &
zenodo:
mkdir -p $(ANALYSIS)/filtered-read-locations/atac/bulk
mkdir -p $(ANALYSIS)/filtered-read-locations/atac/single-nucleus
mkdir -p $(ANALYSIS)/filtered-read-locations/rna
mkdir -p $(ANALYSIS)/atac-peaks/bulk
mkdir -p $(ANALYSIS)/atac-peaks/single-nucleus
mkdir -p $(ANALYSIS)/atac-bedgraphs/single-nucleus
mkdir -p $(ANALYSIS)/atac-bedgraphs/bulk
mkdir -p $(ANALYSIS)/gene-counts
mkdir -p $(ANALYSIS)/clustering
mkdir -p $(ANALYSIS)/luciferase
cp $(DATA)/luciferase/ARL15-rs702634_Luciferase_Rani_12-21-20.xlsx $(ANALYSIS)/luciferase/luciferase.xlsx
cp zenodo-sample-info.txt $(ANALYSIS)/sample-info.txt
cp zenodo-readme.txt $(ANALYSIS)/README.txt
# cluster assignments
cp -L $(WORK)/process-by-cluster/clusters.txt $(ANALYSIS)/clustering/clusters.txt
# umap
cp -L $(WORK)/seurat-joint-2/results/seurat-out/seurat-umap.txt $(ANALYSIS)/clustering/umap.txt
# bedgraphs (starched)
# SN bedgraphs
cp $(foreach g,hg19 rn6,$(foreach c,$(shell seq 0 6),$(WORK)/starch-bdg/results/starch/$(c)-$(g).starch)) $(ANALYSIS)/atac-bedgraphs/single-nucleus/
# Bulk bedgraphs
cp -L $(WORK)/starch-bdg/results/starch/133*.starch $(ANALYSIS)/atac-bedgraphs/bulk/
cp -L $(WORK)/starch-bdg/results/starch/63_*.starch $(ANALYSIS)/atac-bedgraphs/bulk/
cp -L $(WORK)/starch-bdg/results/starch/320-NM-1.starch $(ANALYSIS)/atac-bedgraphs/bulk/HSM1.bulk.rep1.starch
cp -L $(WORK)/starch-bdg/results/starch/320-NM-2.starch $(ANALYSIS)/atac-bedgraphs/bulk/HSM1.bulk.rep2.starch
cp -L $(WORK)/starch-bdg/results/starch/320-NM-3.starch $(ANALYSIS)/atac-bedgraphs/bulk/HSM2.bulk.rep1.starch
cp -L $(WORK)/starch-bdg/results/starch/320-NM-4.starch $(ANALYSIS)/atac-bedgraphs/bulk/HSM2.bulk.rep2.starch
# ATAC-seq peaks. Only use SN peaks.
$(foreach c,$(shell seq 0 6),cp -rL $(WORK)/process-by-cluster/results/peaks/broad/$(c)-*.broadPeak.noblacklist $(ANALYSIS)/atac-peaks/single-nucleus/$(NL))
cp -rL $(WORK)/process-as-bulk/results/macs2/*.broadPeak.noblacklist $(ANALYSIS)/atac-peaks/bulk/
cp -L $(WORK)/bulk-atacseq/results/macs2/320-NM-1_peaks.broadPeak.noblacklist $(ANALYSIS)/atac-peaks/bulk/HSM1.bulk.rep1.broadPeak.noblacklist
cp -L $(WORK)/bulk-atacseq/results/macs2/320-NM-2_peaks.broadPeak.noblacklist $(ANALYSIS)/atac-peaks/bulk/HSM1.bulk.rep2.broadPeak.noblacklist
cp -L $(WORK)/bulk-atacseq/results/macs2/320-NM-3_peaks.broadPeak.noblacklist $(ANALYSIS)/atac-peaks/bulk/HSM2.bulk.rep1.broadPeak.noblacklist
cp -L $(WORK)/bulk-atacseq/results/macs2/320-NM-4_peaks.broadPeak.noblacklist $(ANALYSIS)/atac-peaks/bulk/HSM2.bulk.rep2.broadPeak.noblacklist
# Gene counts
$(foreach m,RNA ATAC,cp -L $(WORK)/quality-nuclei-count-files/results/liger-in/KSM1_$(m).hdf5 $(ANALYSIS)/gene-counts/$(m)-HSM1.counts.h5$(NL))
$(foreach m,RNA ATAC,cp -L $(WORK)/quality-nuclei-count-files/results/liger-in/KSM2_$(m).hdf5 $(ANALYSIS)/gene-counts/$(m)-HSM2.counts.h5$(NL))
$(foreach m,RNA ATAC,cp -L $(WORK)/quality-nuclei-count-files/results/liger-in/rat1_$(m).hdf5 $(ANALYSIS)/gene-counts/$(m)-rat.counts.h5$(NL))
# Read bed files (starched)
cp $(WORK)/make-read-beds/results/starch/*pruned-no-dedup.starch $(ANALYSIS)/filtered-read-locations/rna/
cp $(WORK)/make-read-beds/results/starch/1*.pruned.starch $(ANALYSIS)/filtered-read-locations/atac/single-nucleus/
cp $(WORK)/make-read-beds/results/starch/63*.pruned.starch $(ANALYSIS)/filtered-read-locations/atac/single-nucleus/
cp $(WORK)/make-read-beds/results/starch/320-NM-1.pruned.starch $(ANALYSIS)/filtered-read-locations/atac/bulk/HSM1.bulk.rep1.pruned.starch
cp $(WORK)/make-read-beds/results/starch/320-NM-2.pruned.starch $(ANALYSIS)/filtered-read-locations/atac/bulk/HSM1.bulk.rep2.pruned.starch
cp $(WORK)/make-read-beds/results/starch/320-NM-3.pruned.starch $(ANALYSIS)/filtered-read-locations/atac/bulk/HSM2.bulk.rep1.pruned.starch
cp $(WORK)/make-read-beds/results/starch/320-NM-4.pruned.starch $(ANALYSIS)/filtered-read-locations/atac/bulk/HSM2.bulk.rep2.pruned.starch
# gzip things
cd $(ANALYSIS)/atac-peaks/single-nucleus && gzip *.noblacklist
cd $(ANALYSIS)/atac-peaks/bulk && gzip *.noblacklist
cd $(ANALYSIS)/gene-counts && gzip *.counts.h5
cd $(ANALYSIS)/filtered-read-locations/rna && gzip *
cd $(ANALYSIS) && tar -cvf sn-muscle-processed.tar atac-bedgraphs atac-peaks clustering gene-counts filtered-read-locations luciferase sample-info.txt README.txt
cp zenodo-noreads-readme.txt $(ANALYSIS)/README-no-reads.txt
cp zenodo-reads-readme.txt $(ANALYSIS)/README-reads.txt
cd $(ANALYSIS) && tar -cvf sn-muscle-processed-no-reads.tar atac-bedgraphs atac-peaks clustering gene-counts luciferase sample-info.txt README-no-reads.txt
cd $(ANALYSIS) && tar -cvf sn-muscle-read-locations.tar filtered-read-locations sample-info.txt README-reads.txt