Can you use kallisto to process GRO-seq data?

Question

[LDT]

Dear all,

I was hoping for some input. Can someone use Kallisto to process GRO-seq data in the first steps?

Has anyone tried this before?

[dsull]

Yes, it can (in theory), but, to my knowledge, there is no official workflow for doing so you'll have to come up with one yourself (and show that what you do works correctly).

Since GRO-seq gives nascent RNA, there's a question of what your transcriptome index should be (you probably don't want a cDNA-only index). Also, you should test whether projecting pseudoalignments to genome coordinates (via --genomebam) gives you the expected coverage tracks.

[LDT]

good point dsull! Thank you!