Use Salmon to annotate a Sam file

Question

[Florian Bernard]

Hi,

I was wondering if there was any way to use Salmon to annotate the Sam file, like adding a Tag that says to which transcript the read is mapping to. I think it was a feature available with featureCounts but I can't seem to find anything like that in the documentation of Salmon. And I want to keep using Salmon cause I find it to be more reliable when it comes to transcripts quantification.

I thank you in advance for any input you might have.

Best, Florian

Answer 1

[ATpoint]

See Salmon Alignment-based mode in the manual.

[Florian Bernard]

Honestly I've looked through Salmon's documentation before, and once more, but I can't find any parameters to do what I want to do. Maybe it's just a matter of wording but it would be nice if you could direct me toward what you meant. The closest thing I found is --writeMappings but it doesn't work in alignment-based mode and I'm pretty sure it just outputs the reads that are mapped against a reference. I'm more looking for a way to add a Tag to each reads in the Sam file used as input, just as with Featurecounts. In the end, maybe it's just not possible, but I'd like to be sure about it. Thanks again.