https://github.com/arjunrajlaboratory/RajLabSeqTools
Revision de71c454798747cb321393042871c4b873b8643f authored by Sydney Shaffer on 11 November 2014, 18:56:58 UTC, committed by Sydney Shaffer on 11 November 2014, 18:56:58 UTC
1 parent 5b3f6ce
Tip revision: de71c454798747cb321393042871c4b873b8643f authored by Sydney Shaffer on 11 November 2014, 18:56:58 UTC
Organized the files and wrote a script that runs the samtools, bamutils, and htseq all at once.
Organized the files and wrote a script that runs the samtools, bamutils, and htseq all at once.
Tip revision: de71c45
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
Computing file changes ...