I am trying to use
tximport to get raw count matrices of a bulk RNA-seq sequencing experiment. I followed the tutorial:
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
gencode.vM13.transcripts.fa.sidx. Then when I try getting
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.
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.