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Old 01-12-2020, 01:16 AM   #1
echo manolis
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Default target coverage x gene

Hi,

I have a big list of genes and I want to know the uncovered regions (0X) of each gene (WES data).

In "Genome Browser -> Tools -> Table Browser" I can give as input the gene list and in this way to obtain the coordinates of all exons. Then, I use "bcftools sort" and "bcftools merge" to have the final bed list to use with "samtools depth -a -b ...". At he end I will have the base coverage for all bases of my intervals.

Hoping that it is correct ... the point is that when I go to take all bases with 0X coverage I can not know the gene, only just the coordinates... With which command and file I can give to each coordinate the gene name?

Example of what I want:

HTML Code:
CHR  START COV GENE
chr1 1025  0   CFTR
I only have the first 3 columns and I need also the last one.

Many thanks!
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Old 01-13-2020, 09:10 PM   #2
chobeich
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Hi echo manolis,
Can you post the header of your files?
Greetings
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Old 01-14-2020, 03:35 AM   #3
echo manolis
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Hi,

#intervals_sort_merge.bed

chr7 117119991 117120226
chr7 117144281 117144442
chr7 117149062 117149221
...

#output samtools depth

chr7 117119992 0
chr7 117119993 0
chr7 117119994 0
chr7 117119995 0
...

Last edited by echo manolis; 01-14-2020 at 03:45 AM.
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Old 01-14-2020, 06:52 AM   #4
r.rosati
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Hi! Which platform was used to generate the WES data? If it's an Ion Torrent, some time ago I made this small script for this exact purpose. It can be used with Galaxy if you like.
If it's Ion Torrent data and you want to try it, you'd only need to provide gene names, the BAM file, the Ampliseq targets bedfile, and an annotated source (instructions are in the readme). It will return info on regions fo your genes of interest that are plainly not covered by the panel, and regions with low coverage, strand bias, and low coverage on one strand (the base parameters that can affect basecalling). It also informs you if the poorly covered region is actually within the CDS or splicing regions, or not. And it gives you an easy copy-and-paste text to check the data on IGV.
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Old 01-14-2020, 07:27 AM   #5
echo manolis
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Quote:
Originally Posted by r.rosati View Post
Hi! Which platform was used to generate the WES data? If it's an Ion Torrent, some time ago I made this small script for this exact purpose. It can be used with Galaxy if you like.
If it's Ion Torrent data and you want to try it, you'd only need to provide gene names, the BAM file, the Ampliseq targets bedfile, and an annotated source (instructions are in the readme). It will return info on regions fo your genes of interest that are plainly not covered by the panel, and regions with low coverage, strand bias, and low coverage on one strand (the base parameters that can affect basecalling). It also informs you if the poorly covered region is actually within the CDS or splicing regions, or not. And it gives you an easy copy-and-paste text to check the data on IGV.
Hi r.rosati,

thanks a lot for your reply but they are Illumina data. I was looking for the command to use and the reference list file (maybe gene names with their coordinates ...) in order to create a command for this step.

I will try your tool in the future because some times I have also Ion Torrent data, thanks for the link!

Best
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