https://github.com/arjunrajlaboratory/RajLabSeqTools
Revision 94c2d76a78fa82f8990a3b8977c80cf6957acbcf authored by Sydney Shaffer on 11 November 2014, 14:10:24 UTC, committed by Sydney Shaffer on 11 November 2014, 14:10:24 UTC
1 parent 4e77f9a
Tip revision: 94c2d76a78fa82f8990a3b8977c80cf6957acbcf authored by Sydney Shaffer on 11 November 2014, 14:10:24 UTC
added a line to make the experiment folder if it does not exist
added a line to make the experiment folder if it does not exist
Tip revision: 94c2d76
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
Computing file changes ...