Good Morning, Since StringTie can produce output files for differential expression that can be used by DEseq2 i would like to use it for this. But i got an error during DESeq using the tubular files produce by StringTie
In my case I got 6 sample, I have run Stringtie using a GTF file as a reference and ask it to produce a tabular file for DEseq2 (Transcript counts) for each file.
When I run DESeq2 i got this error:
Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 2122, 2120, 2125, 2138, 2135 Calls: do.call ... eval -> eval -> eval -> .Method -> cbind -> data.frame
It seems to me that each tabular file got different lines number (close to the reference) and for this reason i can't do a Differential Expression analysis with DESeq. Do you know how to solve this problem ?
Thank you very much