I created a txt2gene for Rattus Norvegicus (rnor6) assembly. I downloaded the Ensembl v100 GTF for that ftp://ftp.ensembl.org/pub/release-100/gtf/rattusnorvegicus/Rattusnorvegicus.Rnor_6.0.100.gtf.gz I took only the transcriptID and GeneName:

gtf.gr = rtracklayer::import(gtf.file) # creates a GRanges object
gtf.df = as.data.framegtf.gr)
txt2gene=(gtf.df[gtf.df$type=='transcript' ,c("transcript_id","gene_name")])
names(txt2gene)<-c('TXNAME','GENEID')

The fastq files were quantified using Salmon against the same GTF. When I try to txtimport using

txi <- tximport(files, type="salmon", tx2gene = tx2gene,ignoreTxVersion = TRUE)

I get warnings and error as follows: "missing values for 'group'summarizing counts missing values for 'group'summarizing length missing values for 'group'longer object length is not a multiple of shorter object lengthError in .local(object, ...) : all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE"

I've checked according to another post and I have no duplicated transcripts and no NAs.

sessionInfo() R version 4.0.1 (2020-06-06) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LCCOLLATE=EnglishUnited States.1252 LCCTYPE=EnglishUnited States.1252 LCMONETARY=EnglishUnited States.1252 [4] LCNUMERIC=C LCTIME=English_United States.1252
system code page: 1255

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] readr1.3.1 tximportData1.16.0 tximport1.16.1 EPIC1.1.5

Could you please help me out? What could be wrong?

"Group" here is gene. Are you missing values for GENEID?

Thank you Michael, I've checked only for the TXNAME, didn't think it would be a problem for the GENEID. When I removed those lines indeed everything worked. Thanks, Kerem