https://github.com/arjunrajlaboratory/RajLabSeqTools
Revision 284b48d32da67e457a9e883646325231fe3e31a8 authored by Sydney Shaffer on 12 October 2015, 16:10:07 UTC, committed by Sydney Shaffer on 12 October 2015, 16:10:07 UTC
1 parent c8f87f9
Tip revision: 284b48d32da67e457a9e883646325231fe3e31a8 authored by Sydney Shaffer on 12 October 2015, 16:10:07 UTC
made setup scripts for ATAC data - these unzip fastq files and then concatenate the 4 together (from each lane) for each of the samples.
made setup scripts for ATAC data - these unzip fastq files and then concatenate the 4 together (from each lane) for each of the samples.
Tip revision: 284b48d
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 ...
