bam2fastqc

bam2fastqc.sh

#!/bin/bash

fastqcdir="./FastQC"

if [ -d "$fastqcdir" ];
then
        echo "$fastqcdir available"
else
        mkdir $fastqcdir
fi

for FQ in $(ls *.bam)
do
        #echo $FQ
        bn=$(basename $FQ .bam)
        echo "processing $bn"
        echo
        bam2fastq -q $bn.bam -o $bn\#.fastq
        for i in 1 2
        do
                fastqc --quiet --noextract -o $fastqcdir -t 16 ${bn}_${i}.fastq
                gzip -c  ${bn}_${i}.fastq > ${bn}_${i}.fq.gz
        done
done