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

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4.3 years ago

emmanouil.a ▴ 120

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!

next-gen gene • 693 views

ADD COMMENT • link 4.3 years ago by emmanouil.a ▴ 120

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see Find closest gene to chromosome location

ADD REPLY • link 4.3 years ago by Pierre Lindenbaum 161k

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