Question: Tximport mixing annotations
10 months ago by
Tania • 120
Tania • 120 wrote:
I used the annotation from
"GRCh37_latest_genomic.gff" to build tx2gene while my transcripts are from
txdb <-makeTxDbFromGFF("~/Desktop/work/databases/GRCh37_latest_genomic.gff.gz") k <- keys(txdb, keytype = "GENEID") df <- select(txdb, keys = k, columns = "TXNAME", keytype = "GENEID") tx2gene <- df[, 2:1]
I am getting this error, aren't those files correspond to each other?
Error in summarizeToGene(txi, tx2gene, ignoreTxVersion, countsFromAbundance) : None of the transcripts in the quantification files are present in the first column of tx2gene. Check to see that you are using the same annotation for both.
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