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https://github.com/arjunrajlaboratory/RajLabSeqTools
10 December 2020, 08:13:17 UTC
Revision f267e82b2edd18a28926b84fc23cb2b55bdbc9c3 authored by Ian Mellis on 05 January 2016, 20:38:56 UTC, committed by Ian Mellis on 05 January 2016, 20:38:56 UTC 
Updated runHTSeq.sh to call shared version of hg19.gtf, rather than Syd's in CancerSeq repo. Made a note on Rajlabseqtools pipeline doc.
1 parent f26732e
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Tip revision: f267e82b2edd18a28926b84fc23cb2b55bdbc9c3 authored by Ian Mellis on 05 January 2016, 20:38:56 UTC
Updated runHTSeq.sh to call shared version of hg19.gtf, rather than Syd's in CancerSeq repo. Made a note on Rajlabseqtools pipeline doc.
Tip revision: f267e82
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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