replaced non-ACGT nucleotides

Open GimenaA opened this issue 2 years ago • 1 comments

Hi, This is not an bug, but I'm trying to understand something. I get this message when running salmon quant: "replaced 53 non-ACGT nucleotides with random nucleotides." Can you please explain what this means?

Apr 21 '23 04:04 GimenaA

When there are characters that are not A, C, G, or T in the sequence of the input FASTA file, salmon's FASTA parser replaces them with a base selected uniformly at random from {A, C, G, T}. If you want to see more details, you can take a look at FASTAParser here: https://github.com/COMBINE-lab/salmon/blob/c380f53f1a971775d8a40224694bd889c8c9fc31/src/FASTAParser.cpp#L82

Jun 02 '23 19:06 JuliaHolz