I have a transcriptome assembled de novo, and had its read support evaluated using
Salmon. The transcriptome was constructed to find a couple of genes of interest, which were subsequently identified using
I am looking at the read support for some of these candidates now, and
Salmon indicates that they have 0 reads assigned to them (
NumReads == 0.00).
- How can something be assembled from a set of reads, and not have any reads align to it?
- Can I retain these candidate transcripts for further analysis despite them having 0 read support?
I went through the
Salmon documentation, but I was unable to find any clarifications indicating what this means.