How to get/calculate coverage of a gene using bed file?

Question

[Nikhil]

Hello Everyone,

So I have a Gene Panel with Gene name, I want to calculate gene coverage in a bed file. How can I attain that? I don't have any bam file for that.

I want to check coverage of all genes in the BED file.

[kashiff007]

More explanation needed. how your file looks? whats your desired output would look like?

[Nikhil]

The gene panel I have is just a list of genes and the bed file I have is 3 column bed file i.e chrom position, start and end coordinate. I want to check if those genes is present in that bed file, if yes then how much of the gene is covered by that bed file.

[kashiff007]

In case you have the gene list, you must have annotations of all those genes, usually you can get this information from gff file. Convert this gff into bed file to get the location of all the genes from your list. Now you will have two bed files; one is your gene bed file and other the normal bed file. Now I guess you want to look how your each gene present in your normal bed file. For this purpose use bedtools intersect:

bedtools intersect -a <(sort -k 1,1 -k 2,2n normal_bed_file.bed ) -b <(sort -k 1,1 -k 2,2n gene_bed_file.bed) -wao

For detail you can see the manual page https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html

[Nikhil]

Ohh Thank you for the idea. I'll try and update you.

[Marco Pannone]

Without first a .bam file and then a .bigWig file you cannot obtain any information regarding "gene coverage", even though I am uncertain what you mean for that. Are you dealing with sequencing data?

[Nikhil]

Yes correct without bam file coverage cannot be analysed. I have done coverage analysis using bam files only. But right now I only have a gene list(in excel) and a bed file, from this i have to find how many genes are covered by this said bed file and how much it is covered. Hope this is not confusing, I am a fresher in this field.