wes uncovered regions: how to link the gene name to the uncovered genome coordinates
0
0
Entering edit mode
15 months ago
emmanouil.a ▴ 30

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 • 257 views
ADD COMMENT
1
Entering edit mode
ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Hi, already done this!

ADD REPLY

Login before adding your answer.

Traffic: 1939 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6