Skip to main content

Browse the archive

https://github.com/arjunrajlaboratory/RajLabSeqTools
10 December 2020, 08:13:17 UTC
Revision 2311bee1010fb2075a1866ce75c1b5956ec3859c authored by Sydney Shaffer on 11 November 2014, 19:43:50 UTC, committed by Sydney Shaffer on 11 November 2014, 19:43:50 UTC 
I forgot a variable here - added it back
1 parent 6313ee2
Raw File
Tip revision: 2311bee1010fb2075a1866ce75c1b5956ec3859c authored by Sydney Shaffer on 11 November 2014, 19:43:50 UTC
I forgot a variable here - added it back
Tip revision: 2311bee
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
back to top