problem in cummeRbund

Question

[majeedaasim]

I have run cuffDiff on my data. The out put of the cuffdiff is in a directory named "tx_win_cuffdiff_output". I am trying to analyse it in cummeRbund. The system and R information is as follows:

> platform       x86_64-w64-mingw32          
arch           x86_64                      
os             mingw32                     
system         x86_64, mingw32             
status                                     
major          3                           
minor          4.2                         
year           2017                        
month          09                          
day            28                          
svn rev        73368                       
language       R                           
version.string R version 3.4.2 (2017-09-28)
nickname       Short Summer

I ran the following command after loading cummeRbund library

> (cummeRbund)
cuff <- readCufflinks(dbFile = "cuffData.db", dir="tx_win_cuffdiff_output", gtfFile = "tx_win_cuffdiff_output/transcripts.gtf", genome = "tx_win_cuffdiff_output/SuperDuper.fasta.fasta",rebuild =T)

Following error is shown:

     Creating database tx_win_cuffdiff_output/cuffData.db 
Reading Run Info File tx_win_cuffdiff_output/run.info
Writing runInfo Table
Reading Read Group Info  tx_win_cuffdiff_output/read_groups.info
Writing replicates Table
Reading Var Model Info  tx_win_cuffdiff_output/var_model.info
Writing varModel Table
Reading GTF file
Writing GTF features to 'features' table...
Reading tx_win_cuffdiff_output/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Where did I erred.

Thanks

[WouterDeCoster]

You should know that the old 'Tuxedo' pipeline of Tophat and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.) There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon.

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