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zolotarovgl / GeneExt

GeneExt - Gene extension for improved scRNA-seq data counting
GNU General Public License v3.0
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Request for strandless data implementation #8

Open jkniehaus opened 3 months ago

jkniehaus commented 3 months ago

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

zolotarovgl commented 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

— Reply to this email directly, view it on GitHub https://github.com/zolotarovgl/GeneExt/issues/8, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGZDQJ5NODJKU4NU7NL365TZDZI53AVCNFSM6AAAAABIGL4A46VHI2DSMVQWIX3LMV43ASLTON2WKOZSGMYTGOBRHE4DAOI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

jkniehaus commented 3 months ago

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