scripts to align BY4742 data

This commit includes scripts and setup needed to align the BY4742 ChIPseq data which includes some ABI SOLiD data.

`paper/setup.sh` was updated to create a bowtie colorspace index of sacCer3 for the ABI samples
`paper/.gitignore` was updated to include the BAM alignment output
`paper/BY4742-chipseq/job01_align_data.pbs` is the PBS script to call either BWA or bowtie (as appropriate for sequencing platform used) to align the raw FASTQ data.

Author: owlang

paper/.gitignore

@@ -38,6 +38,7 @@ ENCODE_CellLines/results/ID
 BY4742-chipseq/logs/*.out
 BY4742-chipseq/logs/*.err
 BY4742-chipseq/results/FASTQ
+BY4742-chipseq/results/BAM
 CENPK-chipseq/logs/*.out
 CENPK-chipseq/logs/*.err
 CENPK-chipseq/results/FASTQ

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/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
+