https://github.com/arjunrajlaboratory/RajLabSeqTools
Tip revision: 30d379c8f28dd7e28138a54a824008ec0ba5fc92 authored by Arjun Raj on 29 December 2014, 18:24:55 UTC
Added STARFLAGS to send flags through to STAR.
Added STARFLAGS to send flags through to STAR.
Tip revision: 30d379c
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