Hello all,
I was playing with bedtools intervals to create a genomic interval of my NGS reads and trying to assess the depth of my reads at each interval, so I can create my own GTF file based on this which can cover all reads that I have in my samples.
However in the process I found HTSeq. I have used HTSeq-count earlier to get counts which I used in DE process in DESeq2. Worked great !
But on a different note if I have to do it myself and generate gtf file on my own, the way I described in the first paragraph, can HTSeq genomic interval/ array be an alternative method to bedtool interval?
I am very much new to HTSeq and sort of nai've at that, however I have read through the HTSeq documentation and some parts does seem very similar to what I want to do using bedtools interval, but is it worth the effort in HTSeq or is bedtools better? faster perhaps?
Does anyone have any experience in this arena, who is nice enough to shine some light on this conundrum?
Much appreciated !
geneart.
I was playing with bedtools intervals to create a genomic interval of my NGS reads and trying to assess the depth of my reads at each interval, so I can create my own GTF file based on this which can cover all reads that I have in my samples.
However in the process I found HTSeq. I have used HTSeq-count earlier to get counts which I used in DE process in DESeq2. Worked great !
But on a different note if I have to do it myself and generate gtf file on my own, the way I described in the first paragraph, can HTSeq genomic interval/ array be an alternative method to bedtool interval?
I am very much new to HTSeq and sort of nai've at that, however I have read through the HTSeq documentation and some parts does seem very similar to what I want to do using bedtools interval, but is it worth the effort in HTSeq or is bedtools better? faster perhaps?
Does anyone have any experience in this arena, who is nice enough to shine some light on this conundrum?
Much appreciated !
geneart.