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Question: salmon quantification - identical transcripts in fasta file
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gravatar for dmr210
7 months ago by
dmr2100
dmr2100 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. (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!

ADD COMMENTlink modified 7 months ago by James W. MacDonald45k • written 7 months ago by dmr2100
0
gravatar for James W. MacDonald
7 months ago by
United States
James W. MacDonald45k 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 7 months ago by James W. MacDonald45k
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