wes uncovered regions: how to link the gene name to the uncovered genome coordinates

Question

[emma.a]

Hi,

I have a big list of genes and I found the uncovered regions (0X, WES data). The point is that I have the uncovered genome coordinates but I do not know the related gene names of those coordinates...

In "Genome Browser -> Tools -> Table Browser": I take the coordinates of all exons of the gene list... and I use "bcftools sort" and "bcftools merge" to have the final bed list to use with "samtools dept". At he end I will have the base coverage for all bases of my intervals.

With which tool / command / file I can give to each coordinate the gene name?

Example of what I want:

CHR  START COV GENE
chr1 1025  0   CFTR

I only have the first 3 columns and I need also the last one.

Many thanks!

[Pierre Lindenbaum]

see Find closest gene to chromosome location

[Pierre Lindenbaum]

please review your previous questions (like hg38 Ig regions ) and flag the good answers (green mark on the left).

[emma.a]

Hi, already done this!