https://github.com/arjunrajlaboratory/RajLabSeqTools
Tip revision: cd8eb8168937807ae9dc547aa407e38c9e136aa9 authored by Sydney Shaffer on 20 October 2015, 14:38:01 UTC
changed MACS2 script to run with SPMR parameter
changed MACS2 script to run with SPMR parameter
Tip revision: cd8eb81
unzipAndConcatenateZippedFastq.sh
#!/bin/bash
ZIPFILEDIRECTORY=$1
OUTFASTADIRECTORY=$2
for dirname in $ZIPFIELDIRECTORY/* ; do
cd $dirname
INPUT=`ls *001_R1*`
SAMPLE=${INPUT%%_*}
if [ ! -d $OUTFASTADIRECTORY/raw ]; then
mkdir $OUTFASTADIRECTORY/raw
fi
if [ ! -d $OUTFASTADIRECTORY/raw/$SAMPLE ]; then
mkdir $OUTFASTADIRECTORY/raw/$SAMPLE
fi
for i in *.gz; do
gunzip -c $i > ${i%.*}
done
FASTQR1=${SAMPLE}_R1.fastq
FASTQR2=${SAMPLE}_R2.fastq
cat *R1*fastq > $OUTFASTADIRECTORY/raw/$SAMPLE/$FASTQR1
cat *R2*fastq > $OUTFASTADIRECTORY/raw/$SAMPLE/$FASTQR2
done