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Revision 510a48cb71c018f6afed535d18677686a32cebfe authored by Sydney Shaffer on 12 October 2015, 16:55:45 UTC, committed by Sydney Shaffer on 12 October 2015, 16:55:45 UTC 
updated path to data in submission script
1 parent 284b48d
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unzipAndCat.sh 
#!/bin/bash

EXPERIMENT=$1

for dirname in /home/opadovan/C1_Single_Cell_RNA_Seq-11219209/* ; do
cd $dirname

INPUT=`ls *001_R1*`
SAMPLE=`echo $INPUT | cut -d'_' -f 1`

if [ ! -d $EXPERIMENT/raw ]; then
mkdir $EXPERIMENT/raw
fi

if [ ! -d $EXPERIMENT/raw/$SAMPLE ]; then
mkdir $EXPERIMENT/raw/$SAMPLE
fi

for i in *.gz; do
gunzip -c $i > ${i%.*}
done

FASTQR1=`echo $SAMPLE'_R1.fastq'`
FASTQR2=`echo $SAMPLE'_R2.fastq'`

cat *R1*fastq > $EXPERIMENT/raw/$SAMPLE/$FASTQR1
cat *R2*fastq > $EXPERIMENT/raw/$SAMPLE/$FASTQR2

done
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