Tximport missing values for group summarizing counts
2
0
Entering edit mode
keremwai • 0
@keremwai-23766
Last seen 4.4 years ago

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?

tximport rat reference GTF salmon • 1.3k views
ADD COMMENT
2
Entering edit mode
@mikelove
Last seen 2 days ago
United States

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

ADD COMMENT
0
Entering edit mode
keremwai • 0
@keremwai-23766
Last seen 4.4 years ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 376 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6