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beta6.sh
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#!/bin/bash
#SBATCH -J RNAseq
#SBATCH -o %x.out
#SBATCH -n 12
#SBATCH --mem-per-cpu=18000
source ~/.bash_profile
usage(){
echo "R N A - S E Q W O R K F L O W - @bixBeta"
echo ""
echo ""
echo "Usage: bash" $0 "[-h arg] [-p arg] [-d args] [-t arg] [-g arg] [-r arg] [-s arg] [-c arg]"
echo
echo "---------------------------------------------------------------------------------------------------------------------------"
echo "[-h] --> Display Help"
echo "[-p] --> Project Identifier Number"
echo "[-d] --> Comma Spearated Values for Delimiter and Field <delim,field or default> default: _,5 "
echo "[-t] --> Fastq Trimming <nextSE, nextPE, 4colorSE, miSeqPE, novaPE >"
echo "[-g] --> Reference Genome <hg38, GRCh38, mm10, GRCm38, etc.>"
echo "[-r] --> <SE> <SES> <PE> <PES> <SEBS> <PEBS> <UNMS> or <UNMP> "
echo "[-s] --> Library Strandedness <0, 1, 2> where 1 = first strand, 2 = reverse strand, 0 for unstranded counts "
echo "[-c] --> GeneBody Coverage <yes, no> "
echo "---------------------------------------------------------------------------------------------------------------------------"
echo ""
echo "******************************************** "
echo "**********/ EXTENDED GENOME LIST /********** "
echo "[hg38]=/workdir/genomes/Homo_sapiens/hg38/UCSC/hg38.star"
echo "[mm10]=/workdir/genomes/Mus_musculus/mm10/UCSC/mm10.star"
echo "[GRCh38]=/workdir/genomes/Homo_sapiens/hg38/ENSEMBL/GRCh38.star"
echo "[GRCm38]=/workdir/genomes/Mus_musculus/mm10/ENSEMBL/GRCm38.star"
echo "[cat]=/workdir/genomes/Felis_catus/Felis_catus9.0/Ensembl/genomeDir"
echo "[chicken]=/workdir/genomes/Gallus_gallus/Galgal5/ENSEMBL/galgal5.star"
echo "[chicken6]=/workdir/genomes/Gallus_gallus/Galgal6/ENSEMBL/gtf.102/star.index.102"
echo "[horse]=/workdir/genomes/Equus_caballus/EquCab3/ENSEMBL/genebuild-102/star.index.102"
echo "[horse2]=/workdir/genomes/Equus_caballus/EquCab2/ENSEMBL/EquCab2.star.index"
echo "[ATCC_13047]=/workdir/genomes/Enterobacter_cloacae/ATCC_13047/custom/ATCC_13047.GTF"
echo "[grape]=/workdir/genomes/Vitis_vinifera/GCA_000003745.2/ENSEMBL/Vitis_vinifera.12X.43.bed12"
echo "[rat]=/workdir/genomes/Rattus_norvegicus/rn6/ENSEMBL/rat.star"
echo "[ercc]=/workdir/genomes/contaminants/ERCC_spikeIns/ercc.star"
echo "[lonchura]=/workdir/genomes/Lonchura_striata/LonStrDom1/ENSEMBL/lonchura.star"
echo "[goose]=/workdir/genomes/Anser_brachyrhynchus/ASM259213v1/ENSEMBL/goose.star"
echo "[ehv8]=/workdir/genomes/FastQ_Screen_Genomes/EHV8/ehv8.star"
echo "[erdman]=/workdir/genomes/Mycobacterium_tuberculosis/Erdman_GCA_000350205.1/ENSEMBL/genomeDir"
echo "[TB]=/workdir/genomes/Mycobacterium_tuberculosis/CDC1551_Ensembl/cdc1551.star"
echo "[maize]=/workdir/genomes/Zea_mays/B73_RefGen_v4/ENSEMBL/star.maize"
echo "[finch]=/workdir/genomes/Taeniopygia_guttata/taeGut3.2.4/ENSEMBL/UPDATED.ANNOTS/star.index.updated"
echo "[finch2]=/workdir/genomes/Geospiza_fortis_ground_finch/GeoFor_1.0/NCBI/star.index"
echo "[green]=/workdir/genomes/Chlorocebus_sabaeus/CHlSab1/ENSEMBL/genomeDir"
echo "[dog]=/workdir/genomes/Canis_familiaris/canFam3/ENSEMBL/CanFam3.1.101/genomeDir"
echo "[faba]=/workdir/genomes/Vicia_faba/VfEP_Reference-Unigene/NCBI/genomeDir-wo-gff"
echo "[aphid]=/workdir/genomes/Acyrthosiphon_pisum/pea_aphid_22Mar2018_4r6ur/NCBI/genomeDir"
echo "[cholera]=/workdir/genomes/Vibrio_cholerae/N16961/NCBI/genomeDir"
echo "[BG8]=/workdir/genomes/Methylomicrobium_album_BG8/ASM21427v3/NCBI/custom3-CDS2exon/genomeDir_fixSpaces"
echo "[aedes]=/workdir/genomes/Aedes_aegypti/AaegL5.0/NCBI/AaegL5.0.star"
echo "[aedesVB]=/workdir/genomes/Aedes_aegypti/AaegL5.0/Vectorbase/AaegyptiLVP_AGWG_release49/genomeDir.vectorBase"
echo "[DC3000]=/workdir/genomes/Pseudomonas_syringae/Tomato_DC3000/NCBI/star.index"
echo "[Theileria]=/workdir/genomes/Theileria/Tannulata_ASM322v1/NCBI/starIndex"
echo "[cow]=/workdir/genomes/Bos_taurus/ARS-UCD1.2_GCA_002263795.2/ENSEMBL/star.index"
echo "[salmonella]=/workdir/genomes/Salmonella_enterica/ASM21085v2/NCBI/genomeDir"
echo "[salmonella2]=/workdir/genomes/Salmonella_enterica/ASM2216v1/NCBI/genomeDir"
echo "[EA273]=/workdir/genomes/Erwinia_amylovora/GCF_000091565.1/ncbi/genomeDir"
echo "[ddSmed]=/workdir/genomes/Schmidtea_mediterranea/dd_Smed_v6/NCBI/genomeDir"
echo "[yeast]=/workdir/genomes/Saccharomyces_cerevisiae/R64-1-1_GCA_000146045.2/ENSEMBL/star.index"
echo "[macaca]=/workdir/genomes/Macaca_fascicularis/GCF_000364345.1_Macaca_fascicularis_5.0/NCBI/genomeDir"
echo "[TAIR10]=/workdir/genomes/Arabidopsis_thaliana/TAIR10/ENSEMBL/genomeDir"
echo "[crow]=/workdir/genomes/Corvus_moneduloides/bCorMon1/NCBI/genomeDir"
}
trimSE(){
mkdir TrimQC_stats fastQC trimmed_fastqs
for i in fastqs/*.gz
do
trim_galore -j 8 --nextseq 20 --gzip --length 50 --fastqc --fastqc_args "-t 4 --outdir ./fastQC" $i
done
mv *_trimming_report.txt TrimQC_stats
mv *trimmed.fq.gz trimmed_fastqs
}
trimHiSeq(){
mkdir TrimQC_stats fastQC trimmed_fastqs
for i in fastqs/*.gz
do
trim_galore -j 8 --quality 20 --gzip --length 50 --fastqc --fastqc_args "-t 4 --outdir ./fastQC" $i
done
mv *_trimming_report.txt TrimQC_stats
mv *trimmed.fq.gz trimmed_fastqs
}
trimPE(){
cd fastqs
ls -1 *_R1.fastq* > .R1
ls -1 *_R2.fastq* > .R2
paste -d " " .R1 .R2 > Reads.list
readarray fastqs < Reads.list
mkdir fastQC
for i in "${fastqs[@]}"
do
trim_galore -j 8 --nextseq 20 --gzip --length 50 --paired --fastqc --fastqc_args "-t 4 --outdir ./fastQC" $i
done
mkdir TrimQC_stats trimmed_fastqs
mv *_trimming_report.txt TrimQC_stats
mv *_val* trimmed_fastqs
mv TrimQC_stats fastQC trimmed_fastqs ..
cd ..
}
trimMiSeqPE(){
cd fastqs
ls -1 *_R1_* > .R1
ls -1 *_R2_* > .R2
paste -d " " .R1 .R2 > Reads.list
readarray fastqs < Reads.list
mkdir fastQC
for i in "${fastqs[@]}"
do
trim_galore -j 8 --quality 20 --gzip --length 50 --paired --fastqc --fastqc_args "-t 4 --outdir ./fastQC" $i
done
mkdir TrimQC_stats trimmed_fastqs
mv *_trimming_report.txt TrimQC_stats
mv *_val* trimmed_fastqs
mv TrimQC_stats fastQC trimmed_fastqs ..
cd ..
}
trimNovaPE(){
cd fastqs
ls -1 *_1.fq* > .R1
ls -1 *_2.fq* > .R2
paste -d " " .R1 .R2 > Reads.list
readarray fastqs < Reads.list
mkdir fastQC
for i in "${fastqs[@]}"
do
trim_galore -j 8 --nextseq 20 --gzip --length 50 --paired --fastqc --fastqc_args "-t 4 --outdir ./fastQC" $i
done
mkdir TrimQC_stats trimmed_fastqs
mv *_trimming_report.txt TrimQC_stats
mv *_val* trimmed_fastqs
mv TrimQC_stats fastQC trimmed_fastqs ..
cd ..
}
declare -A genomeDir
genomeDir=( ["hg38"]="/workdir/genomes/Homo_sapiens/hg38/UCSC/hg38.star" \
["mm10"]="/workdir/genomes/Mus_musculus/mm10/UCSC/mm10.star" \
["GRCh38"]="/workdir/genomes/Homo_sapiens/hg38/ENSEMBL/GRCh38.star" \
["GRCm38"]="/workdir/genomes/Mus_musculus/mm10/ENSEMBL/GRCm38.star" \
["cat"]="/workdir/genomes/Felis_catus/Felis_catus9.0/Ensembl/genomeDir" \
["chicken"]="/workdir/genomes/Gallus_gallus/Galgal5/ENSEMBL/galgal5.star" \
["chicken6"]="/workdir/genomes/Gallus_gallus/Galgal6/ENSEMBL/gtf.102/star.index.102" \
["horse"]="/workdir/genomes/Equus_caballus/EquCab3/ENSEMBL/genebuild-102/star.index.102" \
["horse2"]="/workdir/genomes/Equus_caballus/EquCab2/ENSEMBL/EquCab2.star.index" \
["ATCC_13047"]="/workdir/genomes/Enterobacter_cloacae/ATCC_13047/custom/ATCC_13047.GTF" \
["grape"]="/workdir/genomes/Vitis_vinifera/GCA_000003745.2/ENSEMBL/Vitis_vinifera.12X.43.bed12" \
["rat"]="/workdir/genomes/Rattus_norvegicus/rn6/ENSEMBL/rat.star" \
["ercc"]="/workdir/genomes/contaminants/ERCC_spikeIns/ercc.star" \
["lonchura"]="/workdir/genomes/Lonchura_striata/LonStrDom1/ENSEMBL/lonchura.star" \
["goose"]="/workdir/genomes/Anser_brachyrhynchus/ASM259213v1/ENSEMBL/goose.star" \
["ehv8"]="/workdir/genomes/FastQ_Screen_Genomes/EHV8/ehv8.star" \
["erdman"]="/workdir/genomes/Mycobacterium_tuberculosis/Erdman_GCA_000350205.1/ENSEMBL/genomeDir" \
["TB"]="/workdir/genomes/Mycobacterium_tuberculosis/CDC1551_Ensembl/cdc1551.star" \
["maize"]="/workdir/genomes/Zea_mays/B73_RefGen_v4/ENSEMBL/star.maize" \
["finch"]="/workdir/genomes/Taeniopygia_guttata/taeGut3.2.4/ENSEMBL/UPDATED.ANNOTS/star.index.updated" \
["finch2"]="/workdir/genomes/Geospiza_fortis_ground_finch/GeoFor_1.0/NCBI/star.index" \
["green"]="/workdir/genomes/Chlorocebus_sabaeus/CHlSab1/ENSEMBL/genomeDir" \
["dog"]="/workdir/genomes/Canis_familiaris/canFam3/ENSEMBL/CanFam3.1.101/genomeDir" \
["faba"]="/workdir/genomes/Vicia_faba/VfEP_Reference-Unigene/NCBI/genomeDir-wo-gff" \
["aphid"]="/workdir/genomes/Acyrthosiphon_pisum/pea_aphid_22Mar2018_4r6ur/NCBI/genomeDir" \
["cholera"]="/workdir/genomes/Vibrio_cholerae/N16961/NCBI/genomeDir" \
["BG8"]="/workdir/genomes/Methylomicrobium_album_BG8/ASM21427v3/NCBI/custom3-CDS2exon/genomeDir_fixSpaces" \
["aedes"]="/workdir/genomes/Aedes_aegypti/AaegL5.0/NCBI/AaegL5.0.star" \
["aedesVB"]="/workdir/genomes/Aedes_aegypti/AaegL5.0/Vectorbase/AaegyptiLVP_AGWG_release49/genomeDir.vectorBase" \
["DC3000"]="/workdir/genomes/Pseudomonas_syringae/Tomato_DC3000/NCBI/star.index" \
["Theileria"]="/workdir/genomes/Theileria/Tannulata_ASM322v1/NCBI/starIndex" \
["cow"]="/workdir/genomes/Bos_taurus/ARS-UCD1.2_GCA_002263795.2/ENSEMBL/star.index" \
["salmonella"]="/workdir/genomes/Salmonella_enterica/ASM21085v2/NCBI/genomeDir" \
["salmonella2"]="/workdir/genomes/Salmonella_enterica/ASM2216v1/NCBI/genomeDir" \
["EA273"]="/workdir/genomes/Erwinia_amylovora/GCF_000091565.1/ncbi/genomeDir" \
["ddSmed"]="/workdir/genomes/Schmidtea_mediterranea/dd_Smed_v6/NCBI/genomeDir" \
["yeast"]="/workdir/genomes/Saccharomyces_cerevisiae/R64-1-1_GCA_000146045.2/ENSEMBL/star.index" \
["TAIR10"]="/workdir/genomes/Arabidopsis_thaliana/TAIR10/ENSEMBL/genomeDir" \
["crow"]="/workdir/genomes/Corvus_moneduloides/bCorMon1/NCBI/genomeDir" \
["macaca"]="/workdir/genomes/Macaca_fascicularis/GCF_000364345.1_Macaca_fascicularis_5.0/NCBI/genomeDir" )
declare -A bed12
bed12=( ["hg38"]="/workdir/genomes/Homo_sapiens/hg38/UCSC/genes.bed12" \
["mm10"]="/workdir/genomes/Mus_musculus/mm10/UCSC/BED12/mm10.ucsc.bed12" \
["GRCh38"]="/workdir/genomes/Homo_sapiens/hg38/ENSEMBL/Homo_sapiens.GRCh38.bed12" \
["GRCm38"]="/workdir/genomes/Mus_musculus/mm10/ENSEMBL/Mus_musculus.GRCm38.bed12" \
["cat"]="/workdir/genomes/Felis_catus/Felis_catus9.0/Ensembl/Felis_catus.Felis_catus_9.0.95.bed12" \
["chicken"]="/workdir/genomes/Gallus_gallus/Galgal5/ENSEMBL/Gallus_gallus.Gallus_gallus-5.0.bed12" \
["chicken6"]="/workdir/genomes/Gallus_gallus/Galgal6/ENSEMBL/gtf.102/Gallus_gallus.GRCg6a.102.bed12" \
["horse"]="/workdir/genomes/Equus_caballus/EquCab3/ENSEMBL/genebuild-102/Equus_caballus.EquCab3.0.102.bed12" \
["horse2"]="/workdir/genomes/Equus_caballus/EquCab2/ENSEMBL/Equus_caballus.EquCab2.94.BED12" \
["ATCC_13047"]="/workdir/genomes/Enterobacter_cloacae/ATCC_13047/GCF_000025565.1_ASM2556v1_genomic.bed12" \
["grape"]="/workdir/genomes/Vitis_vinifera/GCA_000003745.2/ENSEMBL/Vitis_vinifera.star" \
["rat"]="/workdir/genomes/Rattus_norvegicus/rn6/ENSEMBL/Rattus_norvegicus.Rnor_6.0.bed12" \
["lonchura"]="/workdir/genomes/Lonchura_striata/LonStrDom1/ENSEMBL/Lonchura_striata_domestica.LonStrDom1.bed12" \
["goose"]="/workdir/genomes/Anser_brachyrhynchus/ASM259213v1/ENSEMBL/Anser_brachyrhynchus.ASM259213v1.bed12" \
["maize"]="/workdir/genomes/Zea_mays/B73_RefGen_v4/ENSEMBL/Zea_mays.B73_RefGen_v4.bed12" \
["finch"]="/workdir/genomes/Taeniopygia_guttata/taeGut3.2.4/ENSEMBL/UPDATED.ANNOTS/Taeniopygia_guttata.bTaeGut1_v1.p.bed12" \
["finch2"]="/workdir/genomes/Geospiza_fortis_ground_finch/GeoFor_1.0/NCBI/GCF_000277835.1_GeoFor_1.0_genomic.bed12" \
["dog"]="/workdir/genomes/Canis_familiaris/canFam3/ENSEMBL/CanFam3.1.101/Canis_lupus_familiaris.CanFam3.1.101.bed12" \
["aedes"]="/workdir/genomes/Aedes_aegypti/AaegL5.0/NCBI/GCF_002204515.2_AaegL5.0_genomic.bed12" \
["aedesVB"]="/workdir/genomes/Aedes_aegypti/AaegL5.0/Vectorbase/AaegyptiLVP_AGWG_release49/VectorBase-49_AaegyptiLVP_AGWG.BED12" \
["cow"]="/workdir/genomes/Bos_taurus/ARS-UCD1.2_GCA_002263795.2/ENSEMBL/Bos_taurus.ARS-UCD1.2.BED12" \
["BG8"]="/workdir/genomes/Methylomicrobium_album_BG8/ASM21427v3/NCBI/test/ncbi-genomes-2020-08-27/GCF_000214275.2_ASM21427v3_genomic.bed12" \
["ddSmed"]="/workdir/genomes/Schmidtea_mediterranea/dd_Smed_v6/NCBI/dd_Smed_v6.pcf.bed12" \
["yeast"]="/workdir/genomes/Saccharomyces_cerevisiae/R64-1-1_GCA_000146045.2/ENSEMBL/Saccharomyces_cerevisiae.R64-1-1.bed12" )
align(){
cd trimmed_fastqs
for i in *_trimmed.fq.gz
do
iSUB=`echo $i | cut -d ${DELIMITER} -f${FIELD}`
STAR \
--runThreadN 12 \
--genomeDir ${genomeDir[${DIR}]} \
--readFilesIn $i \
--readFilesCommand gunzip -c \
--outSAMstrandField intronMotif \
--outFilterIntronMotifs RemoveNoncanonical \
--outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix $iSUB. \
--limitBAMsortRAM 61675612266 \
--quantMode GeneCounts
done
# source activate
multiqc -f -n ${PIN}.star.multiqc.report .
mkdir STAR.COUNTS STAR.BAMS STAR.LOGS
mv *.ReadsPerGene.out.tab STAR.COUNTS
mv *.bam STAR.BAMS
mv *.out *.tab *_STARtmp *.list *star.multiqc.report_data STAR.LOGS
mkdir STAR
mv STAR.* *.html STAR
mv STAR ..
cd ..
}
se_split(){
cd trimmed_fastqs
for i in *_trimmed.fq.gz
do
iSUB=`echo $i | cut -d ${DELIMITER} -f${FIELD}`
STAR \
--runThreadN 12 \
--genomeDir ${genomeDir[${DIR}]} \
--readFilesIn $i \
--readFilesCommand gunzip -c \
--outSAMstrandField intronMotif \
--outFilterIntronMotifs RemoveNoncanonical \
--outReadsUnmapped Fastx \
--outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix $iSUB. \
--limitBAMsortRAM 61675612266 \
--quantMode GeneCounts
done
# source activate RSC
multiqc -f -n ${PIN}.starSPLIT.multiqc.report .
mkdir STAR.SPLIT.COUNTS STAR.SPLIT.BAMS STAR.SPLIT.LOGS STAR.SPLIT.Unmapped
mv *Unmapped.out.mate* STAR.SPLIT.Unmapped
cd STAR.SPLIT.Unmapped
for i in *mate*
do
mv $i `echo $i | sed "s/Unmapped/not.$DIR/g"`
done
gzip *mate*
cd ..
mv *.ReadsPerGene.out.tab STAR.SPLIT.COUNTS
mv *.bam STAR.SPLIT.BAMS
mv *.out *.tab *_STARtmp *.list *.multiqc.report_data STAR.SPLIT.LOGS
mkdir STAR.SPLIT
mv STAR.* *.html STAR.SPLIT
mv STAR.SPLIT ..
cd ..
}
alignPE(){
cd trimmed_fastqs
ls -1 *_1.fq.gz > .trR1
ls -1 *_2.fq.gz > .trR2
paste -d " " .trR1 .trR2 > Trimmed.list
readarray trimmedFastqs < Trimmed.list
for i in "${trimmedFastqs[@]}"
do
iSUB=`echo $i | cut -d ${DELIMITER} -f${FIELD}`
STAR \
--runThreadN 12 \
--genomeDir ${genomeDir[${DIR}]} \
--readFilesIn $i \
--readFilesCommand gunzip -c \
--outSAMstrandField intronMotif \
--outFilterIntronMotifs RemoveNoncanonical \
--outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix ${iSUB}. \
--limitBAMsortRAM 61675612266 \
--quantMode GeneCounts
done
# source activate RSC
multiqc -f -n ${PIN}.star.multiqc.report .
mkdir STAR.COUNTS STAR.BAMS STAR.LOGS
mv *.ReadsPerGene.out.tab STAR.COUNTS
mv *.bam STAR.BAMS
mv *.out *.tab *_STARtmp *.list *star.multiqc.report_data STAR.LOGS
mkdir STAR
mv STAR.* *.html STAR
mv STAR ..
cd ..
# cd STAR/STAR.BAMS
# for i in *.bam
# do
# /programs/bin/samtools/samtools index -b $i
# done
# cd ..
# echo
# echo
# pwd
# echo
# echo
# source /programs/RSeQC2-2.6.1/setup.sh
# geneBody_coverage.py -r ${bed12[${DIR}]} -i STAR.BAMS/ -o ${PIN}
# mkdir geneBodyCov
# mv *geneBodyCoverage.* log.txt geneBodyCov
# cd ..
}
pe_split(){
cd trimmed_fastqs
ls -1 *_1.fq.gz > .trR1
ls -1 *_2.fq.gz > .trR2
paste -d " " .trR1 .trR2 > Trimmed.list
readarray trimmedFastqs < Trimmed.list
for i in "${trimmedFastqs[@]}"
do
iSUB=`echo $i | cut -d ${DELIMITER} -f${FIELD}`
STAR \
--runThreadN 12 \
--genomeDir ${genomeDir[${DIR}]} \
--readFilesIn $i \
--readFilesCommand gunzip -c \
--outSAMstrandField intronMotif \
--outFilterIntronMotifs RemoveNoncanonical \
--outSAMtype BAM SortedByCoordinate \
--outReadsUnmapped Fastx \
--outFileNamePrefix ${iSUB}. \
--limitBAMsortRAM 61675612266 \
--quantMode GeneCounts
done
# source activate RSC
multiqc -f -n ${PIN}.starSPLIT.multiqc.report .
mkdir STAR.SPLIT.COUNTS STAR.SPLIT.BAMS STAR.SPLIT.LOGS STAR.SPLIT.Unmapped
mv *Unmapped.out.mate* STAR.SPLIT.Unmapped
cd STAR.SPLIT.Unmapped
for i in *mate*
do
mv $i `echo $i | sed "s/Unmapped/not.$DIR/g"`
done
gzip *mate*
cd ..
mv *.ReadsPerGene.out.tab STAR.SPLIT.COUNTS
mv *.bam STAR.SPLIT.BAMS
mv *.out *.tab *_STARtmp *.list *.multiqc.report_data STAR.SPLIT.LOGS
mkdir STAR.SPLIT
mv STAR.* *.html STAR.SPLIT
mv STAR.SPLIT ..
cd ..
}
pe_bacteria_split(){
cd trimmed_fastqs
ls -1 *_1.fq.gz > .trR1
ls -1 *_2.fq.gz > .trR2
paste -d " " .trR1 .trR2 > Trimmed.list
readarray trimmedFastqs < Trimmed.list
for i in "${trimmedFastqs[@]}"
do
iSUB=`echo $i | cut -d ${DELIMITER} -f${FIELD}`
STAR \
--runThreadN 12 \
--genomeDir ${genomeDir[${DIR}]} \
--readFilesIn $i \
--readFilesCommand gunzip -c \
--outSAMstrandField intronMotif \
--alignIntronMax 1 \
--alignMatesGapMax 45000 \
--outFilterIntronMotifs RemoveNoncanonical \
--outSAMtype BAM SortedByCoordinate \
--outReadsUnmapped Fastx \
--outFileNamePrefix ${iSUB}. \
--limitBAMsortRAM 61675612266 \
--quantMode GeneCounts
done
# source activate RSC
multiqc -f -n ${PIN}.star.multiqc.report .
mkdir STAR.SPLIT.COUNTS STAR.SPLIT.BAMS STAR.SPLIT.LOGS STAR.SPLIT.Unmapped
mv *Unmapped.out.mate* STAR.SPLIT.Unmapped
cd STAR.SPLIT.Unmapped
for i in *mate*
do
mv $i `echo $i | sed "s/Unmapped/not.$DIR/g"`
done
gzip *mate*
cd ..
mv *.ReadsPerGene.out.tab STAR.SPLIT.COUNTS
mv *.bam STAR.SPLIT.BAMS
mv *.out *.tab *_STARtmp *.list *.multiqc.report_data STAR.SPLIT.LOGS
mkdir STAR.SPLIT
mv STAR.* *.html STAR.SPLIT
mv STAR.SPLIT ..
cd ..
}
se_bacteria_split(){
cd trimmed_fastqs
for i in *_trimmed.fq.gz
do
iSUB=`echo $i | cut -d ${DELIMITER} -f${FIELD}`
STAR \
--runThreadN 12 \
--genomeDir ${genomeDir[${DIR}]} \
--readFilesIn $i \
--readFilesCommand gunzip -c \
--outSAMstrandField intronMotif \
--alignIntronMax 1 \
--alignMatesGapMax 45000 \
--outFilterIntronMotifs RemoveNoncanonical \
--outSAMtype BAM SortedByCoordinate \
--outReadsUnmapped Fastx \
--outFileNamePrefix ${iSUB}. \
--limitBAMsortRAM 61675612266 \
--quantMode GeneCounts
done
# source activate RSC
multiqc -f -n ${PIN}.starSPLIT.multiqc.report .
mkdir STAR.SPLIT.COUNTS STAR.SPLIT.BAMS STAR.SPLIT.LOGS STAR.SPLIT.Unmapped
mv *Unmapped.out.mate* STAR.SPLIT.Unmapped
cd STAR.SPLIT.Unmapped
for i in *mate*
do
mv $i `echo $i | sed "s/Unmapped/not.$DIR/g"`
done
gzip *mate*
cd ..
mv *.ReadsPerGene.out.tab STAR.SPLIT.COUNTS
mv *.bam STAR.SPLIT.BAMS
mv *.out *.tab *_STARtmp *.list *.multiqc.report_data STAR.SPLIT.LOGS
mkdir STAR.SPLIT
mv STAR.* *.html STAR.SPLIT
mv STAR.SPLIT ..
cd ..
}
UNMSE() {
cd STAR.SPLIT/STAR.SPLIT.Unmapped/
ls -1 *.mate* > unmapped.list
grepOldRef=`head -1 unmapped.list | grep -o -P '(?<=.not.).*(?=.out.mate*)'`
readarray unmappedSE < unmapped.list
for i in "${unmappedSE[@]}"
do
iSUB=`echo $i | cut -d ${DELIMITER} -f${FIELD}`
#iSUB=`basename $i \.gz`
STAR \
--runThreadN 12 \
--genomeDir ${genomeDir[${DIR}]} \
--readFilesIn $i \
--outSAMstrandField intronMotif \
--alignIntronMax 1 \
--alignMatesGapMax 45000 \
--outReadsUnmapped Fastx \
--readFilesCommand gunzip -c \
--outFilterIntronMotifs RemoveNoncanonical \
--outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix ${iSUB}. \
--limitBAMsortRAM 61675612266 \
--quantMode GeneCounts
done
multiqc -f -n ${PIN}.star.unmapped.${grepOldRef}.mapped.to.${DIR}.multiqc.report .
mkdir STAR.SPLIT.COUNTS STAR.SPLIT.BAMS STAR.SPLIT.LOGS STAR.SPLIT.Unmapped
mv *Unmapped.out.mate* STAR.SPLIT.Unmapped
cd STAR.SPLIT.Unmapped
for i in *Unmapped.out.mate*
do
mv $i `echo $i | sed "s/Unmapped/not.$DIR/g"`
done
gzip *mate*
cd ..
mv *.ReadsPerGene.out.tab STAR.SPLIT.COUNTS
mv *.bam STAR.SPLIT.BAMS
mv *.out *.tab *_STARtmp *.list *.multiqc.report_data STAR.SPLIT.LOGS
mkdir STAR.SPLIT.unmapped.${grepOldRef}.mapped.to.${DIR}
mv STAR.* *.html STAR.SPLIT.unmapped.${grepOldRef}.mapped.to.${DIR}
# mv STAR.SPLIT ..
cd ../../
}
UNMPE() {
cd STAR.SPLIT/STAR.SPLIT.Unmapped/
ls -1 *mate1* > .unR1
ls -1 *mate2* > .unR2
paste -d " " .unR1 .unR2 > unmapped.list
grepOldRef=`head -1 .unR1 | grep -o -P '(?<=.not.).*(?=.out.mate*)'`
readarray unmappedPE < unmapped.list
for i in "${unmappedPE[@]}"
do
iSUB=`echo $i | cut -d ${DELIMITER} -f${FIELD}`
#iSUB=`basename $i \.gz`
STAR \
--runThreadN 12 \
--genomeDir ${genomeDir[${DIR}]} \
--readFilesIn $i \
--outSAMstrandField intronMotif \
--alignIntronMax 1 \
--alignMatesGapMax 45000 \
--outReadsUnmapped Fastx \
--readFilesCommand gunzip -c \
--outFilterIntronMotifs RemoveNoncanonical \
--outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix ${iSUB}. \
--limitBAMsortRAM 61675612266 \
--quantMode GeneCounts
done
multiqc -f -n ${PIN}.star.unmapped.${grepOldRef}.mapped.to.${DIR}.multiqc.report .
mkdir STAR.SPLIT.COUNTS STAR.SPLIT.BAMS STAR.SPLIT.LOGS STAR.SPLIT.Unmapped
mv *Unmapped.out.mate* STAR.SPLIT.Unmapped
cd STAR.SPLIT.Unmapped
for i in *Unmapped.out.mate*
do
mv $i `echo $i | sed "s/Unmapped/not.$DIR/g"`
done
gzip *mate*
cd ..
mv *.ReadsPerGene.out.tab STAR.SPLIT.COUNTS
mv *.bam STAR.SPLIT.BAMS
mv *.out *.tab *_STARtmp *.list *.multiqc.report_data STAR.SPLIT.LOGS
mkdir STAR.SPLIT.unmapped.${grepOldRef}.mapped.to.${DIR}
mv STAR.* *.html STAR.SPLIT.unmapped.${grepOldRef}.mapped.to.${DIR}
# mv STAR.SPLIT ..
cd ../../
}
geneBodyCov(){
cd STAR*/*.BAMS
for i in *.bam
do
BASE=`basename $(echo $i) .Aligned.sortedByCoord.out.bam `
mv $i ${BASE}.bam
done
for i in *.bam
do
/programs/samtools-1.15.1-r/bin/samtools index -b $i
done
cd ..
echo
echo
pwd
echo
echo
source /programs/RSeQC2-2.6.1/setup.sh
geneBody_coverage.py -r ${bed12[${DIR}]} -i *.BAMS/ -o ${PIN}
mkdir geneBodyCov
mv *geneBodyCoverage.* log.txt geneBodyCov
cd ..
}
while getopts "hp:t:g:s:r:c:d:" opt; do
case ${opt} in
h)
echo
echo
echo
usage
echo
echo
exit 1
;;
p )
PIN=$OPTARG
echo "Project Identifier = " $PIN
;;
t )
T=$OPTARG
;;
g)
DIR=$OPTARG
;;
s)
STRAND=$OPTARG
;;
r)
RUN=$OPTARG
;;
c)
GBCOV=$OPTARG
;;
d)
DELIM=$OPTARG
;;
\?)
echo
echo
echo
usage
;;
esac
done
# shift $((OPTIND -1))
#-------------------------------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------------------------------
## check if PIN is provided
if [[ -z "${PIN+x}" ]]; then
PIN="PIN_Null"
fi
#-------------------------------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------------------------------
## check if delimiter parameter exists
if [[ ! -z "${DELIM+x}" ]]; then
#statements
if [[ $DELIM == default ]]; then
DELIMITER="_"
FIELD="5"
echo "file naming will be done using the default delimiter settings"
else
DELIMITER=`echo $DELIM | cut -d , -f1`
FIELD=`echo $DELIM | cut -d , -f2-`
echo "file naming will be done using the delim = $DELIMITER and field = $FIELD settings"
fi
fi
#-------------------------------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------------------------------
## check if trimming parameter exists
if [[ ! -z "${T+x}" ]]; then
#statements
if [[ $T == nextSE ]]; then
trimSE
elif [[ $T == nextPE ]]; then
trimPE
elif [[ $T == 4colorSE ]]; then
trimHiSeq
elif [[ $T == miSeqPE ]]; then
trimMiSeqPE
elif [[ $T == novaPE ]]; then
trimNovaPE
else
echo "-t only accepts nextSE, nextPE, 4colorSE, miSeqPE, novaPE as arguments"
exit 1
fi
fi
#-------------------------------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------------------------------
## check if genomeDir provided
if [[ ! -z "${DIR+x}" ]]; then
if [ ${genomeDir[${DIR}]+_} ]; then
echo Reference genome selected = $DIR
echo
if [[ ! -z "${RUN+x}" ]] && [[ $RUN == "PE" ]]; then
alignPE
elif [[ ! -z "${RUN+x}" ]] && [[ $RUN == "PES" ]]; then
pe_split
elif [[ ! -z "${RUN+x}" ]] && [[ $RUN == "SE" ]]; then
align
elif [[ ! -z "${RUN+x}" ]] && [[ $RUN == "SES" ]]; then
se_split
elif [[ ! -z "${RUN+x}" ]] && [[ $RUN == "UNMS" ]]; then
UNMSE
elif [[ ! -z "${RUN+x}" ]] && [[ $RUN == "UNMP" ]]; then
UNMPE
elif [[ ! -z "${RUN+x}" ]] && [[ $RUN == "PEBS" ]]; then
pe_bacteria_split
elif [[ ! -z "${RUN+x}" ]] && [[ $RUN == "SEBS" ]]; then
se_bacteria_split
else
echo "missing -r option "
usage
exit 1
fi
else
echo "The reference genome provided '"$DIR"' is not available"
echo " OR missing -r "
exit 1
fi
fi
#-------------------------------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------------------------------
## check if strandedness info provided
if [[ ! -z "${STRAND+x}" ]]; then
if [[ $STRAND = "1" ]]; then
echo first strand selected
for i in STAR/STAR.COUNTS/*.ReadsPerGene.out.tab
do
awk 'NR > 4 {print $1 "\t" $3}' $i > $i.rawCounts
done
mkdir STAR/STAR.COUNTS/rawCounts
mv STAR/STAR.COUNTS/*.rawCounts STAR/STAR.COUNTS/rawCounts
elif [[ $STRAND = "2" ]]; then
echo reverse strand selected
for i in STAR/STAR.COUNTS/*.ReadsPerGene.out.tab
do
awk 'NR > 4 {print $1 "\t" $4}' $i > $i.rawCounts
done
mkdir STAR/STAR.COUNTS/rawCounts
mv STAR/STAR.COUNTS/*.rawCounts STAR/STAR.COUNTS/rawCounts
else
echo unstranded selected
for i in STAR/STAR.COUNTS/*.ReadsPerGene.out.tab
do
awk 'NR > 4 {print $1 "\t" $2}' $i > $i.rawCounts
done
mkdir STAR/STAR.COUNTS/rawCounts
mv STAR/STAR.COUNTS/*.rawCounts STAR/STAR.COUNTS/rawCounts
fi
fi
#-------------------------------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------------------------------
## check if run geneBodyCov True
if [[ ! -z "${GBCOV+x}" ]]; then
if [[ $GBCOV = "yes" ]]; then
geneBodyCov
else
echo "geneBodyCov not True"
fi
fi
#-------------------------------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------------------------------
if [[ -z $1 ]] || [[ $1 = "help" ]] ; then
#statements
echo
echo
usage
echo
echo
exit 1
else
echo >> beta6.run.log
echo `date` >> beta6.run.log
echo "Project Identifier Specified = " $PIN >> beta6.run.log
echo "Reference Genome Specified = " $DIR >> beta6.run.log
echo "Trimming for smRNA seq = " $T >> beta6.run.log
echo "SE or PE = " $RUN >> beta6.run.log
echo "Strandedness specified = " $STRAND >> beta6.run.log
echo "GeneBody Coverage = " $GBCOV >> beta6.run.log
echo >> beta6.run.log
echo "ENV INFO: " >> beta6.run.log
echo >> beta6.run.log
echo "trim_galore -j 8 version:"`trim_galore -j 8 --version | grep 'version' | cut -d "n" -f2` >> beta6.run.log
echo "STAR version:" `~/bin/STAR-2.7.0e/bin/Linux_x86_64/STAR --version` >> beta6.run.log
echo "multiqc version:" `~/miniconda2/bin/multiqc --version` >> beta6.run.log
echo "samtools version:" `/programs/bin/samtools/samtools --version` >> beta6.run.log
echo "rseqc version: rseqc=2.6.4 " >> beta6.run.log
echo -------------------------------------------------------------------------------------------------- >> beta6.run.log
fi