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?