multibamcov

multibamcov_signature.sh

+#!/bin/bash
+
+
+bams='results/05-filter_qual_bos_qual25'
+ref='reference/Rank6_Signatures_sorted.bed'
+out='results/05-filter_qual_bos_qual25/multibamc'
+
+mkdir -p $out
+declare -a my_array=("HIGH1_Aligned.sortedByCoord.out.bam HIGH2_Aligned.sortedByCoord.out.bam HIGH3_Aligned.sortedByCoord.out.bam LOW1_Aligned.sortedByCoord.out.bam LOW2_Aligned.sortedByCoord.out.bam LOW3_Aligned.sortedByCoord.out.bam")
+
+
+
+multiBamCov -f 0.1 -bams $bams/HIGH1_Aligned.sortedByCoord.out.bam $bams/HIGH2_Aligned.sortedByCoord.out.bam $bams/HIGH3_Aligned.sortedByCoord.out.bam $bams/LOW1_Aligned.sortedByCoord.out.bam $bams/LOW2_Aligned.sortedByCoord.out.bam $bams/LOW3_Aligned.sortedByCoord.out.bam \
+        -bed $ref > $out/'All_multibamcov.txt';
+
+
+