Multicov

Multicov is a subcommand of the Bedtools software suite used to count sequencing reads that overlap predefined genomic regions across multiple BAM files. It is commonly employed to quantify coverage for regions such as genes, exons, or regulatory elements in several samples in a single run.

Inputs and usage: multicov requires a BED file describing the regions of interest and one or more BAM files containing aligned reads. Typical usage is: bedtools multicov -bams sample1.bam sample2.bam -bed regions.bed. The BAM files should be coordinate-sorted and indexed (with .bai files). The output is a tab-delimited table with one row per region and a column of counts for each input BAM file, preserving the order of the BAMs provided.

Output and interpretation: For each region, multicov reports the number of reads from each BAM that overlap that region. Regions are defined in the BED file using 0-based start coordinates and half-open intervals. A single read may contribute to the count of multiple regions if it overlaps more than one region.

Example: bedtools multicov -bams sample1.bam sample2.bam -bed regions.bed > counts.txt

Related notes: Multicov is useful for preliminary quantification prior to differential analysis or comparative coverage studies. It focuses on overlap counts and does not perform normalization by region length or sequencing depth by itself; downstream methods are typically used for normalization and statistical testing.