Skip to main content

Browse the archive

https://github.com/arjunrajlaboratory/RajLabSeqTools
10 December 2020, 08:13:17 UTC
Revision d6501d6d78c65d29b415c9c8b96298d4d581f418 authored by Arjun Raj on 18 June 2014, 17:12:56 UTC, committed by Arjun Raj on 18 June 2014, 17:12:56 UTC 
Playing with unzip and concatenate fasta.
0 parent
Raw File
Tip revision: d6501d6d78c65d29b415c9c8b96298d4d581f418 authored by Arjun Raj on 18 June 2014, 17:12:56 UTC
Playing with unzip and concatenate fasta.
Tip revision: d6501d6
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