https://github.com/arjunrajlaboratory/RajLabSeqTools
Tip revision: d9be6290d732288cf940aee2b06241427a4dc260 authored by Sydney Shaffer on 11 November 2014, 15:07:01 UTC
added a variable for user name - to make it easier for people to modify this script for their own work
added a variable for user name - to make it easier for people to modify this script for their own work
Tip revision: d9be629
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