bedtools

Question

[upasana]

Hey

I was mapping my bed file that I got from a gff fiile with my .bam files using below command. And I want a .bam output file. Can I get it? And what are the possible output formats here?

bedtools multicov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed  <BED/GFF/VCF>

(got this command from https://bedtools.readthedocs.io/en/latest/content/tools/multicov.html )

Can you please tell me what output formats are possible!

[colindaven]

You map/align a file to a reference genome in general. Here you're not mapping, you're getting coverage counts from previously mapped BAM files.

A bed file contains coordinates so is already mapped.

I don't think any tool will give you bam files from a multicoverage/multisample count assay, since counts are most useful in txt/csv format.

Answer 1

[Carlo Yague]

The output of bedtools multicov is text, and not .bam, as examplified under the link you provided:

bedtools multicov -bams aln1.bam aln2.bam aln3.bam -bed ivls-of-interest.bed
chr1 0       10000   ivl1    100 2234    0
chr1 10000   20000   ivl2    123 3245    1000
chr1 20000   30000   ivl3    213 2332    2034
chr1 30000   40000   ivl4    335 7654    0

It is the only kind of output possible with that command. You wrote that you 'want' a .bam file. Can you explain in more details what you are trying to do ?