Hi every body, I have bam files (in different conditions) and a bed file with specific genes of interest. I would like to calculate the coverage for each bam file over my gene list. What I am doing is, for each condition:
bedtools multicov -bams *cond1.bam -bed exon.bed > multicov_condition1_exon bedtools multicov -bams *cond2.bam -bed exon.bed > multicov_condition2_exon bedtools multicov -bams *cond3.bam -bed exon.bed > multicov_condition3_exon
The final idea is to identified in which condition the coverage is higher. Is that a good option to analyze my data?