Hi guys, I would like to run bedtools multicov on paired (by name) .bam files and .bed files. In other words the situation is the following:
bedtools multicov -bams 1265_29_S1_L001_R1_001.sorted_PCRDuped.bam -bed 1265_29_S1_L001_R1_001_q0.001broad_peaks.bed > 1265_29_S1_L001_R1_001_q0.001_Counts.bed bedtools multicov -bams 1265_30_S1_L001_R1_001.sorted_PCRDuped.bam -bed 1265_30_S1_L001_R1_001_q0.001broad_peaks.bed > 1265_30_S1_L001_R1_001_q0.001_Counts.bed bedtools multicov -bams 1265_31_S1_L001_R1_001.sorted_PCRDuped.bam -bed 1265_31_S1_L001_R1_001_q0.001broad_peaks.bed > 1265_31_S1_L001_R1_001_q0.001_Counts.bed
I have many paired .bam/.bed files. Is there a way to run bedtools multicov by looping over paired .bam/.bed files by matching names? Thank you in advance!