exon.bed file for coverage

Question

[Sabeen]

Hello,

I am trying to find coverage for my exon.bed file. for this i have used bedtools by following code

bedtools bamtobed -i reads.bam | bedtools coverage -a exons.bed -b - > exons.bed.coverage

The exons.bed.coverage file has the following column.

As there are no headings for the columns i am having difficulty in understanding them. I know col A is chr number ,col B and C are start and end points and col E is gene name but I do not understand what columns F,G,H and I are showing.

It would be really great if someone can tell me the header names so that in future i would do my work with understanding.

thanking in advance!

Regards,
sabeen

[mmmmcandrew]

Per the documentation, bedtools coverage will compare two files, A and B, and those columns should relate to:

Column F: The number of features in B that overlapped (by at least one base pair) the A interval

Column G: The number of bases in A that had non-zero coverage from features in B

Column H: The length of the entry in A

Column I: The fraction of bases in A that had non-zero coverage from features in B

However, it's a little unclear to me what you are using as the B file here. It looks like you are converting your reads BAM file to bed correctly, then piping that directly to bedtools coverage, but it's unclear whether you're actually using the reads.bed file as the B file to compare to your exons.bed A file. If you've confirmed that that is the case, the values in columns F-I refer to the exons file, and the amount of coverage of exons you have in your reads.bed file.

[Sabeen]

Thanks a lot for your help. really helped me understand it better.

[mmmmcandrew]

Great! I will post my comment as an answer then.

Answer 1

[mmmmcandrew]

Posting as an answer since this helped the user address their problem:

Per the documentation, bedtools coverage will compare two files, A and B, and those columns should relate to:

Column F: The number of features in B that overlapped (by at least one base pair) the A interval

Column G: The number of bases in A that had non-zero coverage from features in B

Column H: The length of the entry in A

Column I: The fraction of bases in A that had non-zero coverage from features in B

However, it's a little unclear to me what you are using as the B file here. It looks like you are converting your reads BAM file to bed correctly, then piping that directly to bedtools coverage, but it's unclear whether you're actually using the reads.bed file as the B file to compare to your exons.bed A file. If you've confirmed that that is the case, the values in columns F-I refer to the exons file, and the amount of coverage of exons you have in your reads.bed file.