Open jkniehaus opened 3 months ago
Hi Jesse!
Indeed, the tool isn’t supposed to work with unstranded data, but it should be fairly easy to add this functionality.
Can you drop me an email: @.*** ? I’d need some sample of the data to see how it looks like and to try some things out.
Thanks, Grisha
On Thu, 23 May 2024 at 22:49, Jesse Niehaus @.***> wrote:
Hello, Thanks for the tool! I appreciate having the choice to not extend into an overlapping gene. I have a BAM from RNA-seq data that is not strand aware but is still 3' enriched. Would it be possible to choose not to UTR extension if there's a gene on the antisense strand? I imagine this might get tricky if two genes overlap entirely, but this would be desirable in my case to make sure I'm quantifying expression in the appropriate gene.
Thanks! Jesse
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Thanks for the quick response, Grisha! My email is kylius0@gmail.com I have can subset a bam to a few million reads generated from STAR. They're paired-end, which might be problematic.
I appreciate it! Jesse
Hello, Thanks for the tool! I appreciate having the choice to not extend into an overlapping gene. I have a BAM from RNA-seq data that is not strand aware but is still 3' enriched. Would it be possible to choose not to UTR extension if there's a gene on the antisense strand? I imagine this might get tricky if two genes overlap entirely, but this would be desirable in my case to make sure I'm quantifying expression in the appropriate gene.
Thanks! Jesse