Question: salmon quantification - identical transcripts in fasta file
0
gravatar for dmr210
2.4 years ago by
dmr21020
dmr21020 wrote:

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. (seeĀ 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!

salmon • 582 views
ADD COMMENTlink modified 2.4 years ago by James W. MacDonald50k • written 2.4 years ago by dmr21020
Answer: salmon quantification - identical transcripts in fasta file
0
gravatar for James W. MacDonald
2.4 years ago by
United States
James W. MacDonald50k wrote:

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.

ADD COMMENTlink written 2.4 years ago by James W. MacDonald50k
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