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10 December 2020, 08:13:14 UTC
Revision 425610ffb041dc289503471489a9435be01bc2a1 authored by Ian Mellis on 07 January 2016, 19:25:08 UTC, committed by Ian Mellis on 07 January 2016, 19:25:08 UTC
Adding step to melt count data from all samples from an experiment to a single tsv file
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Tip revision: 425610ffb041dc289503471489a9435be01bc2a1 authored by Ian Mellis on 07 January 2016, 19:25:08 UTC
Adding step to melt count data from all samples from an experiment to a single tsv file
Tip revision: 425610f
unzipAndConcatenateZippedFastq.sh 
#!/bin/bash

ZIPFILEDIRECTORY=$1

OUTFASTQDIRECTORY=$2

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

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

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

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

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

    if [ ! -e $OUTFASTQDIRECTORY/raw/$SAMPLE/$FASTQR1 ]; then
        echo Working on $SAMPLE
        for i in *.gz; do
            gunzip -c $i > ${i%.*}
        done


        cat *fastq > $OUTFASTQDIRECTORY/raw/$SAMPLE/$FASTQR1
    #    cat *R2*fastq > $OUTFASTQDIRECTORY/raw/$SAMPLE/$FASTQR2
    fi
done