Export coverage Track from IGV

Question

[MarVi]

Hi all,

I would like to know if there is any way to get the total count of reads for each position in the genome from the track "coverage" in IGV? I want to extract the counts of reads for each position depending on the strand of the alignment.

This is because, I wanted to use genomecov in order to get the information for each strand of the genome. But, despite il seemed a good idea, it wasn't because for each position it counts the reads that have some kind of splicing. So, for example, for the first position in the image, it's going to count 3 reads when there is only one read overlapping the first position, and so on !

So, it seems to me, when I look at the coverage track from IGV, that it displays the correct count.

But if it's not possible to export that coverage, Is there any other way to retain only the count for the real reads that are overlapping each position in the genome, taking into account each strand?

Thanks in advance!

[cpad0112]

It is possible to export strand specific coverage track from IGV.

1. You can export coverage for each position for both the strands, for all the bases, for each position
2. You can export coverage for each position for both the strands, for each of the bases (ATGCN) for each position
3. You can export strand specific coverage for each position, for all the bases or for each position. Strand specific information has two options: 'read' or 'first'. 'read' Separates count by 'read' strand, 'first' uses the first in pair strand.

Read the manual here: https://github.com/etal/IGV/blob/master/docs/igvtools_readme.txt

[MarVi]

I don't think that this is exactly what I was looking for, mainly because : "The count command computes average feature density over a specified window size across the genome." and "The output file, which can be binary "tdf" or ascii "wig" format."

[cpad0112]

That window can be 1 base. That is how one gets coverage for position (overall coverage or base wise overage). Here OP was asking for strand specific coverage as well. wig format is tab separated format.

[MarVi]

Sorry! Maybe I am newly in this, but what do you mean for "Here OP was asking for strand specific coverage as well"? Please. I already have run the process but I don't know how to differentiate the strands.

[cpad0112]

copy/pasted from OP (OP=Original post/poster) I want to extract the counts of reads for each position depending on the strand of the alignment.

counts of each reads for each position - overall coverage (cumulative coverage for all bases) or base wise coverage. at any given position. This can be extracted by keeping window size 1 in igvtools

depending on the strand of the alignment - IGVtools provides too kinds of strand specific read information- First in pair and read strand.