Can I force Sierra to include exons from gtf?

VCCRI / Sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data

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Can I force Sierra to include exons from gtf? #71

Closed HenriettaHolze closed 3 months ago

HenriettaHolze commented 3 months ago

Hi, I ran Sierra as described in the vignette and successfully "called" potential novel exons that I wasn't able to look at before.
However, I would also like to look at known exons. Sierra did not include some known exons despite (few) reads mapping to it. Can I force Sierra to respect the exons specified in the gtf file?

Thanks!

rj-patrick commented 3 months ago

Hi @HenriettaHolze,

Yes that's possible. You will need to add the exon coordinates yourself as 'peaks' to the peak file and rerun the counting on that updated file. And the AnnotatePeaksFromGTF function as well on the updated peak file.

Cheers, Ralph

HenriettaHolze commented 3 months ago

Great, thanks!