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https://github.com/arjunrajlaboratory/RajLabSeqTools
10 December 2020, 08:13:17 UTC
Revision 3ad90f05fa0acafab6fafac654b71d266e5953d7 authored by Sydney Shaffer on 24 November 2015, 20:55:21 UTC, committed by Sydney Shaffer on 24 November 2015, 20:55:21 UTC 
Changed folder names and the appropriate files to make things a bit clearer in the ATAC analysis. Specifically, the stepThreeHOMERpeaks folder was renamed to stepFourHOMERpeaks.
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Tip revision: 3ad90f05fa0acafab6fafac654b71d266e5953d7 authored by Sydney Shaffer on 24 November 2015, 20:55:21 UTC
Changed folder names and the appropriate files to make things a bit clearer in the ATAC analysis. Specifically, the stepThreeHOMERpeaks folder was renamed to stepFourHOMERpeaks.
Tip revision: 3ad90f0
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
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