My lab uses Salmon to align / quantify our bulk RNAseq data. It typically runs without a hitch, but recently we've had two patient derived xenograft samples, with a mix of mouse and human DNA, give the message:
Run human only on original .fasta
Our PDX runs typically output a separate graft (human) and host (mouse) counts matrix, but for some reason these two samples do not. Has anyone faced this issue before? Any help / tips would be greatly appreciated, as I can't seem to find any mention of this error message in the code on GitHub, on StackOverflow, or here on BioStars.