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https://github.com/arjunrajlaboratory/RajLabSeqTools
10 December 2020, 08:13:17 UTC
Revision 30d379c8f28dd7e28138a54a824008ec0ba5fc92 authored by Arjun Raj on 29 December 2014, 18:24:55 UTC, committed by Arjun Raj on 29 December 2014, 18:24:55 UTC 
Added STARFLAGS to send flags through to STAR.
1 parent 7202e48
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Tip revision: 30d379c8f28dd7e28138a54a824008ec0ba5fc92 authored by Arjun Raj on 29 December 2014, 18:24:55 UTC
Added STARFLAGS to send flags through to STAR.
Tip revision: 30d379c
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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