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huangyh09 / brie

BRIE: Bayesian Regression for Isoform Estimate in Single Cells
https://brie.readthedocs.io
Apache License 2.0
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Is BRIE2 appliable in 10x Genomics scRNA data #63

Closed cynthier closed 7 months ago

cynthier commented 8 months ago

"Naturally, protocols such as CEL-seq or STRT-seq that bias reads towards the ends of the transcript cannot provide information about exon-skipping events that may be very far from the ends of a transcript."

I saw this in BRIE article, and I am not sure whether BRIE2 can be used in 10x Genomics scRNA data which also is PolyA-tailed mRNA data.

huangyh09 commented 7 months ago

Hi, thanks for the question.

From version 2.2.2, the answer is yes (but it also depends on the splicing events you are interested in), see the updates in the manual.

This new setting is generic for any two-isoform annotations, no matter where the alternative exons are. However, since the sequencing is biased, you may see very limited coverage of exon-skipping, while if you are interested in the exon changes near the poly-A site, the chance will be larger. You may take Fig. 4D in this work as an example of how BRIE2 can work with 10x Genomics data.

Yuanhua

huangyh09 commented 7 months ago

BTW, if you are particularly interested in the alternative poly-A site, we are working on a new tool specifically for that and may be available in ~2 months. Stay tuned.

cynthier commented 7 months ago

Thank you so much! @huangyh09

cynthier commented 7 months ago

BTW, if you are particularly interested in the alternative poly-A site, we are working on a new tool specifically for that and may be available in ~2 months. Stay tuned.

Look forward to your great work!