Question: Creating StringTie output that meets DESeq expected input content for DE analysis
0
gravatar for Lorenzo.Pavarini
5 months ago by
Lorenzo.Pavarini20 wrote:

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

Lorenzo

rna-seq deseq stringtie • 398 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by Lorenzo.Pavarini20
2
gravatar for Lorenzo.Pavarini
5 months ago by
Lorenzo.Pavarini20 wrote:

I found the solution. Among the StringTie Parameters I select yes in "Use Reference transcripts only" and in this case i got same line numbers in each file

ADD COMMENTlink written 5 months ago by Lorenzo.Pavarini20

Hi Lorenzo,

Very glad you sorted out the problem. Thank you for posting it back to help others!

Jen, Galaxy team

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
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