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Merge pull request #15 from CEGRcode/datasets
Run StrainID on BY4742 ChIPseq data
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‎paper/.gitignore‎

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ENCODE_CellLines/results/BAM
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ENCODE_CellLines/results/BAM-nospike
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ENCODE_CellLines/results/ID
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BY4742-chipseq/logs/*.out
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BY4742-chipseq/logs/*.err
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BY4742-chipseq/results/FASTQ
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BY4742-chipseq/results/BAM
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BY4742-chipseq/results/ID
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CENPK-chipseq/logs/*.out
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CENPK-chipseq/logs/*.err
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CENPK-chipseq/results/FASTQ

‎paper/BY4742-chipseq/README‎

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

‎paper/BY4742-chipseq/SraRunInfo.csv‎

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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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SRR3497399,2017-05-11 00:00:55,2016-05-11 11:04:54,67640691,3281838684,0,48,1816,GCF_000146045.2,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3497399/SRR3497399.1,SRX1756249,Hsf1_ChIP,ChIP-Seq,ChIP,GENOMIC,SINGLE,0,0,ABI_SOLID,AB 5500xl-W Genetic Analysis System,SRP074822,PRJNA321111,,321111,SRS1432863,SAMN04966256,simple,4932,Saccharomyces cerevisiae,Hsf1_ChIP,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,F73F96964C383156F61A669AC0074AD9,443BEFEC858B5AF9C065249419528A69
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SRR3497410,2017-05-11 00:00:55,2016-05-11 11:08:21,80694279,3905823162,0,48,2028,GCF_000146045.2,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3497410/SRR3497410.1,SRX1756250,Hsf1_input,ChIP-Seq,unspecified,GENOMIC,SINGLE,0,0,ABI_SOLID,AB 5500xl-W Genetic Analysis System,SRP074822,PRJNA321111,,321111,SRS1432864,SAMN04966257,simple,4932,Saccharomyces cerevisiae,Hsf1_input,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,C76260FC0AED0743E40E038EEC232960,D96A93109D0C695D8263594CD89E9473
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SRR3497446,2017-05-11 00:00:55,2016-05-17 11:46:57,56996253,8537022864,56996253,149,3350,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497446/SRR3497446.1,SRX1756259,Hsf1_t0_0.05U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432872,SAMN04966258,simple,4932,Saccharomyces cerevisiae,Hsf1_t0_0.05U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,1D79B28E58E73793E3F2416BE52FC99B,A4C02F8943A763A0C413FF046BA716B5
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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
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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
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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
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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
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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
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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
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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
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‎paper/BY4742-chipseq/job/00_download_data.pbs‎

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

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

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

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

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

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# logfiles from STDERR and STDOUT of running job files go here

‎paper/BY4742-chipseq/results/README‎

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# Downloaded FASTQ files and StrainID results go here

‎paper/README‎

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|--ENCODEdata-CellLines
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|--HIV_samples
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|--YKOC-wgs
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|--BY4742-chipseq
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|--CENPK-chipseq
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## YKOC-wgs
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contains the scripts and information for downloading, processing, and running DeletionID on the Puddu et al, 2019 dataset for identifying deletions
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## BY4742-chipseq
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contains the scripts and information for downloading, processing, and running StrainID on the BAM files
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## CENPK-chipseq
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contains the scripts and information for downloading, processing, and running StrainID on the
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contains the scripts and information for downloading, processing, and running StrainID on the BAM files

‎paper/setup.sh‎

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