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https://github.com/arjunrajlaboratory/RajLabSeqTools
10 December 2020, 08:13:17 UTC
Revision 30d379c8f28dd7e28138a54a824008ec0ba5fc92 authored by Arjun Raj on 29 December 2014, 18:24:55 UTC, committed by Arjun Raj on 29 December 2014, 18:24:55 UTC 
Added STARFLAGS to send flags through to STAR.
1 parent 7202e48
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Tip revision: 30d379c8f28dd7e28138a54a824008ec0ba5fc92 authored by Arjun Raj on 29 December 2014, 18:24:55 UTC
Added STARFLAGS to send flags through to STAR.
Tip revision: 30d379c
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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