Degradome seq

bowhan edited this page Apr 12, 2016 · 7 revisions

piPipes Degradome/RACE/CAGE-seq pipeline

This document explains how to run piPipes Degradome/CAGE/RACE-seq pipeline and how to interpret the output.

This pipeline provides analysis on (1) abundance (2) 5' feature and (3) relative distance to piRNAs for genes and transposons derived, 5' mono-phosphated transcripts using single-end or paired-end Degradome-seq reads generated by Next Generation Sequencing.

Example 1. Run single Degradome-seq library

Install the mouse mm9 genome, if you haven't done so

# require internet access
piPipes install -g mm9

Download Degradome-seq and small RNA-seq (optional) sample data from NCBI SRA

# use fastq-dump from SRATools (http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software)
# to download data and convert to fastq; require internet access
fastq-dump -F --gzip -A Pillai.CAGE.miwi_het.testis.adult SRR363963

# to analyze the cleavage signature between small RNA and degradome/RACE, we also need
# download the small RNA-seq data for the same/similar sample
fastq-dump -F -Z SRR363958 | \
  cutadapt -a TCGTATGCCG -O 6 -m 18 --discard-untrimmed - | \
  gzip > Pillai.SRA.wild_type.testis.adult.trimmed.fq.gz

Check usage message

piPipes deg
# or
piPipes deg -h

Using default parameters, without small RNA related analysis

# -i: input fastq or gzipped fastq for the degradome-seq (single-end)
# -g: use mouse genome mm9
# -c: number of CPUs to use
# -o: output directory
piPipes deg \
  -i Pillai.CAGE.miwi_het.testis.adult.fastq.gz \
  -g mm9 \
  -c 8 \
  -o Pillai.CAGE.miwi_het.testis.adult.piPipes_out \
  1> Pillai.CAGE.miwi_het.testis.adult.piPipes.stdout \
  2> Pillai.CAGE.miwi_het.testis.adult.piPipes.stderr

Run the pipeline with small RNA analysis (recommended)

The purpose of degradome cloning in piRNA field is to capture the cleavage product of PIWI proteins. However, due to the ubiquitousness of 5' monophosphate and the instability of cleavage product, only a small portion of the reads correspond to the cleavage product. Then it is necessary to analyze the relative 5' to 5' distance between small RNA and degradome reads.

# Run small RNA pipeline first
# -i: input small RNA sequencing data in Fastq or gzipped Fastq format
# -g: use mouse genome mm9
# -c: number of CPUs to use
# -o: output directory
piPipes small \
  -i Pillai.SRA.wild_type.testis.adult.trimmed.fq.gz \
  -g mm9 \
  -o Pillai.SRA.wild_type.testis.adult.piPipes_output \
  -c 8 \
  1> Pillai.SRA.wild_type.testis.adult.piPipes.stdout \
  2> Pillai.SRA.wild_type.testis.adult.piPipes.stderr

# Run degradome pipeline with small RNA data
# -i: input Fastq or gzipped Fastq for the degradome-seq (single-end)
# -g: use mouse genome mm9
# -c: number of CPUs to use
# -o: output directory
# -s: directory with small RNA pipeline output
piPipes deg \
  -i Pillai.CAGE.miwi_het.testis.adult.fastq.gz \
  -g mm9 \
  -s Pillai.SRA.wild_type.testis.adult.piPipes_output \
  -c 8 \
  -o Pillai.CAGE.miwi_het.testis.adult.piPipes_out \
  1> Pillai.CAGE.miwi_het.testis.adult.piPipes.stdout \
  2> Pillai.CAGE.miwi_het.testis.adult.piPipes.stderr

Interpretation of the output files

The output directory should contain the following folders and files:

cufflinks_output/
htseq_count/
rRNA_mapping/
input_read_files/
genome_mapping/
bigWig/
summaries/
pdfs/
bedtools_count/
gene_transposon_cluster_direct_mapping/
map_small_RNA/
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.basic_stats
bowtie_index/

rRNA_mapping/ contains log files of rRNA mapping using Bowtie2

Similar to RNA-seq, degradome pipeline also removes rRNA mappable reads first.

genome_mapping/ contains output for genome mapping

# STAR output
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.SJ.out.tab
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.Log.progress.out
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.Log.out
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.Log.final.out
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.Unmapped.out.mate1
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.STAR.log

# genome alignment file in bam format, sorted by coordinates
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.bam
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.bam.bai

# genome alignment file in bed12 format
# since degradome/CAGE requires the 5' end of the reads being precisely mapped
# alignments with soft-clipping on the 5' ends are removed
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.unique.bed12
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.bed12

# "unique bead12" file contains only unique mappers
# each line is an alignment of a sequence
$ head Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.unique.bed12
chr10	3218970	3219075	HWUSI-EAS702:65:FC:1:32:14333:13809	1	+	3218970	3219075	255,0,0	1	105	0
chr10	3218970	3219075	HWUSI-EAS702:65:FC:1:8:5133:15456	1	+	3218970	3219075	255,0,0	1	105	0
chr10	3218970	3219075	HWUSI-EAS702:65:FC:1:15:18950:16133	1	+	3218970	3219075	255,0,0	1	105	0
chr10	3218970	3219075	HWUSI-EAS702:65:FC:1:33:3872:8475	1	+	3218970	3219075	255,0,0	1	105	0
chr10	3218970	3219075	HWUSI-EAS702:65:FC:1:11:2584:14460	1	+	3218970	3219075	255,0,0	1	105	0
chr10	3218970	3219075	HWUSI-EAS702:65:FC:1:15:9578:3676	1	+	3218970	3219075	255,0,0	1	105	0
chr10	3218970	3219075	HWUSI-EAS702:65:FC:1:28:10944:3671	1	+	3218970	3219075	255,0,0	1	105	0
chr10	3218970	3219075	HWUSI-EAS702:65:FC:1:6:13520:3867	1	+	3218970	3219075	255,0,0	1	105	0
chr10	3218970	3219075	HWUSI-EAS702:65:FC:1:18:14786:3150	1	+	3218970	3219075	255,0,0	1	105	0
chr10	3218970	3219075	HWUSI-EAS702:65:FC:1:29:18350:4783	1	+	3218970	3219075	255,0,0	1	105	0

# "all bed12" file contains signals from all mappers
# each line is no longer an alignment but accumulated signal from a species alignment
# field 4:  accumulated signal from multi count. for example, 26 means that there are
# 26 reads from the library can be mapped here; but they could be mapped to elsewhere as well
# field 5:  accumulated signal from reads that have been apportioned to the number
# of loci they can be mapped to. For example, if a read can be mapped to 2 loci, its contribution
# is 0.5. And from all the 26 reads that can be mapped here, their contribution is 0.999...
$ head Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.bed12
chr1	100010440	100010544	26	0.999999000000000415334	-	100010440	100010544	1	1	104	0
chr1	100011803	100011908	1	0.0384615000000000026303	+	100011803	100011908	2	1	105	0
chr1	100089433	100089521	3	3	-	100089433	100089521	3	1	88	0
chr1	100101123	100101228	1	0.142857000000000011752	-	100101123	100101228	4	1	105	0
chr1	100101492	100101597	1	1	-	100101492	100101597	5	1	105	0
chr1	100101531	100101636	1	0.0500000000000000027756	-	100101531	100101636	6	1	105	0
chr1	10015089	10017223	58	58	-	10015089	10017223	7	2	55,40	0,2094
chr1	100181199	100181293	1	0.333332999999999990415	+	100181199	100181293	8	1	94	0
chr1	100184297	100184402	28	1.55263279999999959102	+	100184297	100184402	9	1	105	0
chr1	100187852	100187957	1	0.0151515000000000000374	+	100187852	100187957	10	1	105	0

bedtools_count/ contains nucleotide percentage surrounding different genomic features. If small RNA data is provided, the pipeline also calculates the "cis Ping-Pong" signature between small RNA and degradome. See the pdfs/ folder for the figure output.

# the data are used to draw percentage plots in pdfs folder
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.x_rpmk_MASK.bed12
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.x_rpmk_MASK.bed12.intersect_with_hybrid_piRNA_Cluster_EXON.species.5end_60.percentage
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.x_rpmk_MASK.bed12.intersect_with_prepachytene_piRNA_Cluster_EXON.species.5end_60.percentage
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.x_rpmk_MASK.bed12.intersect_with_Zamore_NR_EXON.species.5end_60.percentage

bigWig/ contains bigWig files that can be used in UCSC genome browser.

summaries/ contains summary files with statistics on different genomic feature. Note that tRNA, snoRNA et al. has been removed before doing the interacting analysis. Thus the counts in the summary table are smaller than the one in the basic.stats file.

feature	total_lib_all_mapper_reads	total_feature_all_mapper_reads	feature_all_mapper_percentage	\
feature_sense_all_mapper_reads	feature_antisense_all_mapper_reads	feature_all_mapper_sense_fraction	\
total_lib_unique_mapper_reads	total_feature_unique_mapper_reads	feature_unique_mapper_percentage	\
feature_sense_unique_mapper_reads	feature_antisense_unique_mapper_reads	\
feature_unique_mapper_sense_fraction	total_lib_unique_mapper_species	\
total_feature_unique_mapper_species	feature_unique_mapper_percentage	\
feature_sense_unique_mapper_species	feature_antisense_unique_mapper_species	\
feature_unique_mapper_sense_fraction
piRNA_Cluster_EXON	3643781	86474	0.024	79067	7407	0.914	49220	84057	1.708	76909	7148	0.915	47436	7722	0.163	7072	650	0.916
prepachytene_piRNA_Cluster_EXON	3643781	4931	0.001	4785	146	0.970	49220	4726	0.096	4590	136	0.971	47436	509	0.011	498	11	0.978
hybrid_piRNA_Cluster_EXON	3643781	4720	0.001	4410	310	0.934	49220	4694	0.095	4385	309	0.934	47436	494	0.010	479	15	0.970
pachytene_piRNA_Cluster_EXON	3643781	76824	0.021	69872	6952	0.910	49220	74637	1.516	67934	6703	0.910	47436	6719	0.142	6095	624	0.907

gene_transposon_cluster_direct_mapping/ contains direct mapping output to transcriptome (gene + piRNA cluster + transposon concensus sequence) as well as abundance evaluation by eXpress

# mapping output
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.gene+cluster+repBase.log
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.gene+cluster+repBase.bam

# abundance estimation by eXpress
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.gene+cluster+repBase.eXpress.log
results.xprs
params.xprs

bowtie_index/ contains bowtie index build from degradome reads themselves or the sequence retrieved from the genome surrounding the 5' end of degradome reads. They are used as an index for small RNA mapping. The coordinates tell the relative distance between small RNA and degradome.

# index was build from the degradome directly; if paired-end is used, only the \1 read is used.
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.4.ebwt
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.3.ebwt
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.1.ebwt
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.2.ebwt
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.rev.1.ebwt
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.rev.2.ebwt

# 200 nucleotide surrounding the 5' end of the degradome reads were taken out, reverse-
# complemented and used to build an index for small RNA to map
# the index was build from degradome reads assigned to different genomie features
# Note that one coordinate is used once, even more than one read can be mapped to
# this coordinate.
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.rev.2.bt2

map_small_RNA/ contains the mapping result of small RNA to (1) degradome index; (2) 401 nt (200 x 2 + 1) index

# mapping of small RNA directly to the degradome index
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.bed2
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.species.5end
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.reads.5end
# mapping of small RNA to the 401 nt index
# from left to right: distance to the cleavage site, + mapping 5' end (guide strand), - mapping 5' end (cleaved strand)
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.species

pdfs/ contain the pdf outputs

Please see example figures from the Github Wiki page or our manuscript.

##Flowchart and example figures from our manuscript


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