https://github.com/arjunrajlaboratory/RajLabSeqTools
Revision bfa05d7fd7f85712805e2c2d4dfe5c41628bb472 authored by Sydney Shaffer on 24 November 2015, 21:03:05 UTC, committed by Sydney Shaffer on 24 November 2015, 21:03:05 UTC
1 parent aa7fecf
Tip revision: bfa05d7fd7f85712805e2c2d4dfe5c41628bb472 authored by Sydney Shaffer on 24 November 2015, 21:03:05 UTC
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Tip revision: bfa05d7
unzipAndConcatenateZippedFastq.sh
#!/bin/bash
ZIPFILEDIRECTORY=$1
OUTFASTADIRECTORY=$2
for dirname in $ZIPFIELDIRECTORY/* ; do
cd $dirname
INPUT=`ls *001_R1*`
SAMPLE=${INPUT%%_*} # Cuts filename string after first '_'
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 ...