Hi,

I am using Salmon to quantify transcript expression based on RNAseq.

I am using the ensembl annotation, and as I am interested in non-coding RNA (lncRNA in particular) I merged the "cdna.all" and the "ncrna" fasta files. (see ftp://ftp.ensembl.org/pub/release-87/fasta/mus_musculus/)

After looking at these two transcriptomes in more details, I found that 20 transcripts are common between the two files, i.e. they have the same ID.

My question is relatively silly... but I wasn't able to answer it based on the dicumentation:

Would Salmon get 'confused' by this and consider the reads as ambiguous in some way, or would it 'notice' that the ID is identical and 'ignore' the repetition?

Thanks!

This support site is intended for Bioconductor packages. Salmon isn't a Bioconductor package (it's not even an R package!), so you are in the wrong place. You should ask the developers, or look at their FAQ.