I have used
Salmon on some new RNAseq data that includes a host and virus (human and virus). When indexing the transcriptome, I concatenated the virus genome (as they don't have transcriptomes) to the .fatsa file of the host. I did the same with the .gtf file used for building the
txdb object. However, following the
tximport the virus is not included in the counts object.
I believe the issue is when constructing the tx2gene tibble, as there is no
TXNAME for the virus...
#construct a tx v. gene name tibble
k <- keys(txdb, keytype = "TXNAME")
tx2gene <- AnnotationDbi::select(txdb, k, "GENEID", "TXNAME")
Any suggestions for a work around for this? I would really like to compare the virus counts per sample :)