Run StrainID on BY4742 ChIPseq data

paper/.gitignore

@@ -35,6 +35,11 @@ SyntheticStrain/results/hg19*
 ENCODE_CellLines/results/BAM
 ENCODE_CellLines/results/BAM-nospike
 ENCODE_CellLines/results/ID
+BY4742-chipseq/logs/*.out
+BY4742-chipseq/logs/*.err
+BY4742-chipseq/results/FASTQ
+BY4742-chipseq/results/BAM
+BY4742-chipseq/results/ID
 CENPK-chipseq/logs/*.out
 CENPK-chipseq/logs/*.err
 CENPK-chipseq/results/FASTQ

paper/BY4742-chipseq/README

@@ -0,0 +1,13 @@
+# Run StrainID on BY4742 datasets to evaluate StrainID's ability to detect the variant-based strain background
+
+# "Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters"
+# (de Jonge et al, 2017)
+
+# GEO accession: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81787
+
+# The default sacCer3 StrainID database is used
+# Download data using SRA accessions using `job/00_download_data.pbs`
+# Align FASTQ files and process using `job/01_align_data.pbs`
+# Run StrainID on BAM inputs using `job/02_run_StrainID.pbs` to determine if StrainID can successfully identify the strain background
+
+#specifically look into performance in distinguishing two closesly related strains: BY4741 and BY4742

paper/BY4742-chipseq/SraRunInfo.csv

@@ -0,0 +1,12 @@
+Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash
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+SRR3497452,2017-05-11 00:00:56,2016-05-11 11:24:59,62257597,9364630504,62257597,150,3611,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497452/SRR3497452.1,SRX1756270,Hsf1_t0_0.2U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432882,SAMN04966260,simple,4932,Saccharomyces cerevisiae,Hsf1_t0_0.2U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,103A6282A4032934D6050C6DD2B5E6BF,871F9BAEC203D09E57EB5726F7A84CD1
+SRR3497453,2017-05-11 00:00:56,2016-05-11 12:06:21,61425579,9217294875,61425579,150,3523,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497453/SRR3497453.1,SRX1756274,Hsf1_t0_0.8U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432886,SAMN04966262,simple,4932,Saccharomyces cerevisiae,Hsf1_t0_0.8U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,851EA8BF587B0C7F08802CD998CA5246,5BDD7B50B89F79F3CEC01DA4ABA31660
+SRR3497454,2017-05-11 00:00:56,2016-05-11 12:01:49,48284496,7235073133,48284496,149,2828,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497454/SRR3497454.1,SRX1756275,Hsf1_t0_3.0U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432887,SAMN04966264,simple,4932,Saccharomyces cerevisiae,Hsf1_t0_3.0U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,220B1999B9CB4227F5A35B51BCC72724,2F01C0E9269BD0FA1523461BC01D8198
+SRR3497449,2017-05-11 00:00:56,2016-05-11 13:19:10,53608235,8028655564,53608235,149,3153,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497449/SRR3497449.1,SRX1756263,Hsf1_t30_0.05U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432875,SAMN04966259,simple,4932,Saccharomyces cerevisiae,Hsf1_t30_0.05U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,A5A12C5FFFE69D3ABB4F0C42AE0FF7EA,5D151CA79CC01ACCE3C98CF5E646DD47
+SRR3497456,2017-05-11 00:00:56,2016-05-11 14:19:38,62404674,9388451136,62404674,150,3646,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos1/sra-pub-run-8/SRR3497456/SRR3497456.1,SRX1756283,Hsf1_t30_0.2U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432895,SAMN04966261,simple,4932,Saccharomyces cerevisiae,Hsf1_t30_0.2U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,4D316816A01301B7B30F9CC1381B5018,DDDB3A1D0A7A3F6255418B0C27D316E6
+SRR3497459,2017-05-11 00:00:56,2016-05-11 14:21:03,70846857,10638854137,70846857,150,4074,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497459/SRR3497459.1,SRX1756286,Hsf1_t30_0.8U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432898,SAMN04966263,simple,4932,Saccharomyces cerevisiae,Hsf1_t30_0.8U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,9C84D57EE58BF1B09AF37E3504851620,C6850B43795D5AF9504DF7A5F4625B13
+SRR3497461,2017-05-11 00:00:56,2016-05-11 15:19:34,52591831,7857035482,52591831,149,3032,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos1/sra-pub-run-8/SRR3497461/SRR3497461.1,SRX1756287,Hsf1_t30_3.0U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432899,SAMN04966265,simple,4932,Saccharomyces cerevisiae,Hsf1_t30_3.0U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,00F78D41D1508EDEFAC4DE473028A626,6EB7361E2E83CF786951734E6596C8F0
+

paper/BY4742-chipseq/job/00_download_data.pbs

@@ -0,0 +1,33 @@
+#!/bin/bash
+#PBS -l nodes=1:ppn=6
+#PBS -l pmem=24gb
+#PBS -l walltime=03:00:00
+#PBS -A open
+#PBS -o logs/download.data.log.out
+#PBS -e logs/download.data.log.err
+#PBS -t 1-10
+
+# Requires
+# parallel fastq dump v2.8.0
+
+# FIRST CHANGE PATH TO EXECUTE
+WRK=/path/to/GenoPipe/paper/BY4742-chipseq
+cd $WRK
+
+module load anaconda3
+source activate ~/work/myconda/genopipe/
+
+[ -d logs ] || mkdir logs
+[ -d results/FASTQ ] || mkdir -p results/FASTQ
+
+INDEX=$(($PBS_ARRAYID+1))
+
+METADATA=SraRunInfo.csv
+INFO=`sed "${INDEX}q;d" $METADATA`
+SRR=`echo $INFO | cut -d"," -f1`
+#echo $INFO
+
+# FASTQ-DUMP
+echo "($INDEX) Begin downloading $SRR FASTQ..."
+parallel-fastq-dump --gzip --split-files -t 8 -O results/FASTQ -s $SRR
+echo "Complete"

paper/BY4742-chipseq/job/01_align_data.pbs

@@ -0,0 +1,57 @@
+#!/bin/bash
+#PBS -l nodes=1:ppn=4
+#PBS -l pmem=16gb
+#PBS -l walltime=02:00:00
+#PBS -A open
+#PBS -o logs/align.data.log.out
+#PBS -e logs/align.data.log.err
+#PBS -t 1-10
+
+module load gcc
+module load samtools
+module load bwa
+module load anaconda3
+source activate ~/work/myconda/genopipe/
+
+# FIRST CHANGE PATH TO EXECUTE
+WRK=/path/to/GenoPipe/paper/BY4742-chipseq
+cd $WRK
+
+[ -d logs ] || mkdir logs
+[ -d results/BAM ] || mkdir -p results/BAM
+[ -d results/uniq-BAM ] || mkdir -p results/uniq-BAM
+
+YGENOME=$WRK/../input/sacCer3.fa
+CSGENOME=$WRK/../input/sacCer3_index
+
+INDEX=$(($PBS_ARRAYID+1))
+
+METADATA=SraRunInfo.csv
+INFO=`sed "${INDEX}q;d" $METADATA`
+SRR=`echo $INFO | cut -d"," -f1`
+SAMPLE=`echo $INFO | cut -d"," -f12`
+PLATFORM=`echo $INFO | cut -d"," -f19`
+#PAIR=`echo $INFO | cut -d"," -f16`
+#echo $INFO
+
+FQ=$WRK/results/FASTQ/$SRR
+BAM=$WRK/results/BAM/$SAMPLE
+
+echo "($PBS_ARRAYID) Aligned $SRR $PLATFORM reads > $BAM"
+if [[ " $PLATFORM " =~ " ABI_SOLID " ]]; then
+	bowtie -C -S $CSGENOME <(gzip -dc $YGENOME $FQ\_1.fastq.gz) \
+		| samtools sort \
+		> $BAM.bam
+	echo "(PBS_ARRAYID) $BAM single aligned (bowtie color space)"
+elif [[ " $PLATFORM " =~ " ILLUMINA " ]]; then
+	bwa mem $YGENOME $FQ\_1.fastq.gz $FQ\_2.fastq.gz -t 4 \
+		| samtools sort \
+		> $BAM.bam
+	echo "($PBS_ARRAYID) $BAM pair aligned (BWA)"
+fi
+
+#samtools view -b -F4 $BAM > $WRK/results/uniq-BAM/$SAMPLE.bam
+
+echo "($PBS_ARRAYID) Indexing..."
+samtools index $BAM.bam
+echo "($PBS_ARRAYID) Complete!"

paper/BY4742-chipseq/job/02_indexed_runSID.pbs

@@ -0,0 +1,52 @@
+#!/bin/bash
+#PBS -l nodes=1:ppn=6
+#PBS -l pmem=24gb
+#PBS -l walltime=03:00:00
+#PBS -A open
+#PBS -o logs/sid.log.out
+#PBS -e logs/sid.log.err
+#PBS -t 1-10
+
+module load anaconda3
+source activate genopipe
+
+# FIRST CHANGE PATH TO EXECUTE
+WRK=/path/to/GenoPipe/paper/BY4742-chipseq
+cd $WRK
+
+[ -d logs ] || mkdir logs
+[ -d results/ID ] || mkdir -p results/ID
+
+INDEX=$(($PBS_ARRAYID+1))
+
+METADATA=SraRunInfo.csv
+INFO=`sed "${INDEX}q;d" $METADATA`
+SAMPLE=`echo $INFO | cut -d"," -f12`
+#echo $INFO
+
+# Store directory paths
+DATABASE=$WRK/../db/sacCer3_VCF
+GENOME=$WRK/../input/sacCer3.fa
+SEED=$PBS_ARRAYID
+GENOPIPE=$WRK/../..
+
+BAM=$WRK/results/BAM/$SAMPLE
+#BAM=$WRK/results/uniq-BAM/$SAMPLE
+ID=$WRK/results/ID/
+
+# Set-up Temp directory
+TEMP=$WRK/temp-$PBS_ARRAYID
+[ -d $TEMP ] || mkdir $TEMP
+cd $TEMP
+ln -s $BAM.bam
+ln -s $BAM.bam.bai
+
+## Execute Single StrainID and record time
+cd $GENOPIPE/StrainID
+echo "**Begin executing StrainID for ${SAMPLE}..."
+{ time bash identify-Strain.sh -i $TEMP -g $GENOME -v $DATABASE -s $SEED -o $ID > $ID/$SAMPLE.std ; } 2> $ID/$SAMPLE.time
+echo "...single StrainID for ($PBS_ARRAYID) ${SAMPLE} finished."
+
+## Clean-up
+rm -r $TEMP
+

paper/BY4742-chipseq/logs/README

@@ -0,0 +1 @@
+# logfiles from STDERR and STDOUT of running job files go here

paper/BY4742-chipseq/results/README

@@ -0,0 +1 @@
+# Downloaded FASTQ files and StrainID results go here

paper/README

@@ -16,6 +16,7 @@ paper
 |--ENCODEdata-CellLines
 |--HIV_samples
 |--YKOC-wgs
+|--BY4742-chipseq
 |--CENPK-chipseq
 
 
@@ -55,5 +56,8 @@ contains the scripts and information for downloading, processing, and running Ep
 ## YKOC-wgs
 contains the scripts and information for downloading, processing, and running DeletionID on the Puddu et al, 2019 dataset for identifying deletions
 
+## BY4742-chipseq
+contains the scripts and information for downloading, processing, and running StrainID on the BAM files
+
 ## CENPK-chipseq
-contains the scripts and information for downloading, processing, and running StrainID on the 
+contains the scripts and information for downloading, processing, and running StrainID on the BAM files

paper/setup.sh

@@ -13,8 +13,10 @@
 
 # Required software:
 # wget
+# Python 3
 # Perl 5.18+
 # bwa v0.7.14+
+# bowtie v1.2.3
 #
 # Optional software:
 # twoBitToFa
@@ -149,3 +151,8 @@ cd $WRK/db
 ln -s ../../StrainID/sacCer3_VCF
 ln -s ../../StrainID/hg19_VCF
 cd $WRK
+
+# Setup color-space index for yeast genome
+# (used by BY4742-chipseq)
+bowtie-build -C input/sacCer3.fa input/sacCer3_index
+