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:
I only have the first 3 columns and I need also the last one.
Many thanks!
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
Many thanks!
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