diff --git a/Adapting_new_script_for_computing_cluster.sh b/Adapting_new_script_for_computing_cluster.sh index 3a91d69..a182d95 100755 --- a/Adapting_new_script_for_computing_cluster.sh +++ b/Adapting_new_script_for_computing_cluster.sh @@ -148,10 +148,10 @@ execute() { map=$(grep -Po '[0-9, /.]*% overall alignment rate' $id.mappingStats.txt | grep -Po '[0-9,/.]*') mapFrac=$(printf "%.4f" $(echo $map / 100 | bc -l)) dedup=$(printf "%.4f" $(grep -Po 'Unknown Library.*' dedup/${id}_dedupMetric.txt | awk '{print $10}')) - filtered=$(expr $(samtools view -c dedup/${id}_dedup.bam) / 2) - fripReads=$(expr $(bedtools intersect -a dedup/${id}_dedup.bam -b dedup_peaks/${id}_peaks.narrowPeak -u -ubam | samtools view -c) / 2) + filtered=$(( $(samtools view -c dedup/${id}_dedup.bam) / 2 )) + fripReads=$(( $(bedtools intersect -a dedup/${id}_dedup.bam -b dedup_peaks/${id}_peaks.narrowPeak -u -ubam | samtools view -c) / 2 )) FRiP=$(printf "%.4f" $(echo $fripReads / $filtered | bc -l)) - peaks=$(expr $(wc -l <"dedup_peaks/${id}_peaks.narrowPeak") - 1) + peaks=$(( $(wc -l <"dedup_peaks/${id}_peaks.narrowPeak") - 1 )) echo -e "$id\t$fragments\t$filtered\t$mapFrac\t$dedup\t$FRiP\t$peaks" >> cnt_gata_qc_metrics.txt # Here I have no idea how to transfer this