I am trying to use tximport
to get raw count matrices of a bulk RNA-seq sequencing experiment. I followed the tutorial:
https://bioconductor.org/packages/3.7/bioc/vignettes/tximport/inst/doc/tximport.html
Where they generate tx2gene
in the following way:
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
k <- keys(txdb, keytype = "TXNAME")
tx2gene <- select(txdb, k, "GENEID", "TXNAME")
So, I reasoned to do it the same way. But since my data is mouse one, I used a different gene annotation file:
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
k <- keys(txdb, keytype = "TXNAME")
tx2gene <- select(txdb, k, "GENEID", "TXNAME")
The transcript annotation file that I used when running salmon
is gencode.vM13.transcripts.fa.sidx
. Then when I try getting txi
object:
txi <- tximport(files, type = "salmon", tx2gene = tx2gene)
It raises the error:
Seems like I am creating tx2gene
in the wrong way. Maybe I need to use a different library, not TxDb.Mmusculus.UCSC.mm10.knownGene
. Any suggestions would be greatly appreciated.
Update
I looked into the quant.sf
files that I got from salmon
and it looked the following way:
A colleague adviced me to strip away everything that follows the dot in the Name
column, so it started to look:
However, still no luck. The identifiers in the k <- keys(txdb, keytype = "TXNAME")
look like that:
"uc007afg.1" "uc007afh.1" "uc007afi.2" "uc011wht.1" "uc011whu.1"
"uc057aty.1"
I suppose I need to convert these identifiers first to ENS
-like ones, but do not know how to.