search

COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
https://combine-lab.github.io/salmon
GNU General Public License v3.0
777 stars 165 forks source link

Alevin - annotate for RNA velocity (request) #353

Closed caleblareau closed 4 years ago

caleblareau commented 5 years ago

This would be super useful if you could pull it off... My sense would be that one could add an annotation in the bam tags and then quantify at the end of the computation...

http://velocyto.org/

roryk commented 5 years ago

To do this you'd need to do whole genome alignments or otherwise align to genes with introns since the RNA velocity it looking at intronic counts to estimate the amount of pre-mRNA in the cell.

k3yavi commented 4 years ago

My apologies for the late reply. Please checkout our latest preprint here. We explore the intricacies with generating unspliced counts and/or RNA velocity in detail .