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https://github.com/arjunrajlaboratory/RajLabSeqTools
10 December 2020, 08:13:17 UTC
Revision de71c454798747cb321393042871c4b873b8643f authored by Sydney Shaffer on 11 November 2014, 18:56:58 UTC, committed by Sydney Shaffer on 11 November 2014, 18:56:58 UTC 
Organized the files and wrote a script that runs the samtools, bamutils, and htseq all at once.
1 parent 5b3f6ce
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Tip revision: de71c454798747cb321393042871c4b873b8643f authored by Sydney Shaffer on 11 November 2014, 18:56:58 UTC
Organized the files and wrote a script that runs the samtools, bamutils, and htseq all at once.
Tip revision: de71c45
unzipAndConcatenateZippedFastq.sh 
#!/bin/bash

ZIPFILEDIRECTORY=$1

OUTFASTADIRECTORY=$2

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

    INPUT=`ls *001_R1*`
    SAMPLE=${INPUT%%_*}

    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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