Entering edit mode
11.1 years ago
l0o0
▴
220
I try to use the makeTranscriptDbFromGFF function of GenomicFeatures to creat a TranscriptDb object. I do as the tutorial
when i run the cmd:
> chrominfo = data.frame(
+ chrome=c('Chr1','Chr2','Chr3','Chr4','Chr5','Chr6','Chr7'),
+ length=c(29149675,23174626,39782674,23425844,28023477,29076228,19226500),
+ is_circular=c(FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE))
>
> txdb = makeTranscriptDbFromGFF(file='Cucumber_v2i.gff3',
+ format='gff3',
+ exonRankAttributeName='exon_number',
+ chrominfo=chrominfo,
+ dataSource='SoLab',
+ species='Cucumis sativus Linn')
there is a error:
Error in DataFrame(...) : different row counts implied by arguments
Calls: makeTranscriptDbFromGFF ... standardGeneric -> eval -> eval -> eval -> .Method -> DataFrame
Execution halted
How can figure it out? any advice will be appreciated, thank you
Hi jeales! I corrent the chrome to chrom. I find that exonRankAttributeName causes the error. It is ok now after i remove the exonRankAttributeName. But i think the gff3 file has exon rank info. part of my gff3 file:
Does the string 'Csa1M000010.1.exon1/2/3' specify the exon rank?
You don't need to specify an exon rank attribute. It's best to let makeTranscriptDbFromGFF() work out the exon rank for you. Exons are usually ordered correctly in GFFs. Unless you know your GFF has exons in the wrong order, i'd remove the exonRankAttributeName.
Yeah, I remove the exon rank, it is ok now.