Skip to main content
https://github.com/arjunrajlaboratory/RajLabSeqTools
10 December 2020, 08:13:14 UTC
Revision e576e76099a5992d0cbfea3b28d91e5c398e7d21 authored by Sydney Shaffer on 24 November 2015, 22:05:43 UTC, committed by Sydney Shaffer on 24 November 2015, 22:05:43 UTC
renamed a poorly named script
1 parent bfa05d7
Raw File Download Save again
Tip revision: e576e76099a5992d0cbfea3b28d91e5c398e7d21 authored by Sydney Shaffer on 24 November 2015, 22:05:43 UTC
renamed a poorly named script
Tip revision: e576e76
unzipAndConcatenateZippedFastq.sh 
#!/bin/bash

ZIPFILEDIRECTORY=$1

OUTFASTADIRECTORY=$2

for dirname in $ZIPFIELDIRECTORY/* ; do
    cd $dirname

    INPUT=`ls *001_R1*`
    SAMPLE=${INPUT%%_*}  # Cuts filename string after first '_'

    if [ ! -d $OUTFASTADIRECTORY/raw ]; then
        mkdir $OUTFASTADIRECTORY/raw
    fi

    if [ ! -d $OUTFASTADIRECTORY/raw/$SAMPLE ]; then
        mkdir $OUTFASTADIRECTORY/raw/$SAMPLE
    fi

    for i in *.gz; do
        gunzip -c $i > ${i%.*}
    done

    FASTQR1=${SAMPLE}_R1.fastq
    FASTQR2=${SAMPLE}_R2.fastq

    cat *R1*fastq > $OUTFASTADIRECTORY/raw/$SAMPLE/$FASTQR1
    cat *R2*fastq > $OUTFASTADIRECTORY/raw/$SAMPLE/$FASTQR2

done