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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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Using GeneExt for 5 prime #4

Closed tatyana-perlova closed 8 months ago

tatyana-perlova commented 8 months ago

We would be very interested in trying out your tool, however most of our data comes from 5' chemistry. How difficult would it be to adapt your GeneExt to use it with 5' scRNAseq? Thanks a lot!

zolotarovgl commented 8 months ago

Hi, Tatyana!

Unfortunately, most of the functions in the tool have been written in a way to extend in the 3' direction. For the 5' application one would have to re-write the tool considerably. What are the rates for intergenic reads do you get in your system? Are there visible peaks associated with the genes that are not overlapped by genes' 5'-ends? If that's the widespread issue for 5'-technology, we may consider implementing 5'-version later.