https://github.com/arjunrajlaboratory/RajLabSeqTools
Revision 8f355a9ee069f4f290cca29d0c7c2e6a33e4f2ec authored by Sydney Shaffer on 15 October 2015, 12:18:38 UTC, committed by Sydney Shaffer on 15 October 2015, 12:18:38 UTC
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Tip revision: 8f355a9ee069f4f290cca29d0c7c2e6a33e4f2ec authored by Sydney Shaffer on 15 October 2015, 12:18:38 UTC
made scripts to run MACS2
Tip revision: 8f355a9
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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