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chip_sample_processing.sh
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chip_sample_processing.sh
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#! /bin/bash
SAMPLE_DIR=$1
i=$2
NUM_SAMPLES=$3
INS_DIR=$4
ANALYSIS=$5
BROAD=$6
PAIRED=$7
UPSTREAM=$8
DOWNSTREAM=$9
MOTIFLENGTH=${10}
MOTIFSIZE=${11}
NUM_EXP=${12}
EXP_DESIGN=${13}
CHR=${14}
echo ""
echo " --Yep this is chip_sample_processing.sh for sample $i all right!"
echo ""
cd $SAMPLE_DIR
## Sample quality control and read mapping to reference genome
if [ $PAIRED -eq 0 ]
then
echo ""
echo " --Oh nice, you got UNPAIRED data! Less work for me!"
echo ""
echo ""
echo " --Firstly let's see how good these reads are with some FASTQC:"
echo ""
fastqc chip_$i.fastq.gz
echo ""
echo " --Now let's map these bad boys to the reference genome with BOWTIE2:"
echo ""
bowtie2 -x ../../genome/index -U chip_$i.fastq.gz -S chip_$i.sam
else
echo ""
echo " --Oh man, you got PAIRED data for real? That's twice the work!!"
echo ""
echo ""
echo " --Firstly let's see how good these reads are with some FASTQC:"
echo ""
fastqc chip_${i}_1.fastq.gz
fastqc chip_${i}_2.fastq.gz
echo ""
echo " --Now let's map these bad boys to the reference genome with BOWTIE2:"
echo ""
bowtie2 -x ../../genome/index -1 chip_${i}_1.fastq.gz -2 chip_${i}_2.fastq.gz -S chip_$i.sam
fi
## Generating sorted bam file
echo ""
echo " --Let me index you this sam file to a nice bam and bam.bai with SAMTOOLS:"
echo ""
samtools sort -o chip_$i.bam chip_$i.sam
rm chip_$i.sam
rm *.fastq.gz
samtools index chip_$i.bam
echo ""
echo " --Chip $i processing DONE!!"
echo ""