Question: Cuffdiff Error after cuffmerge or cuffcompare
0
gravatar for romualdomf
2.6 years ago by
romualdomf0
romualdomf0 wrote:

Hi everyone, I'm doing a transcriptome of zebrafish, 2 replicates for each condition of 3 conditions. Trimmed adapters and low quality, fastq groomed, and mapped with tophat using the reference genome. So assembled with cufflinks every replicate with genome annotation and reference, but when i tried to merge with cuffmerge I got an error, a friend said to me to redo cufflinks step without annotation and reference, and use reference and anotation on cuffmerge step. And it worked, but when i try cuffdiff with the cuffmerge transcripts I got an error, tried use cuffcompare instead of cuffmerge but got error on cuffdiff too (final of log error below) and i dont know what is it, i tried precompute expressions with cuffquant and use de cxb instead of tophat bams, got error too, someone can help ?

 

Reading ./gene_exp.diff
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "integer"'
Calls: readCufflinks ... make.db.names -> .valueClassTest -> is -> <Anonymous>
In addition: Warning message:
attributes are not identical across measure variables; they will be dropped 
Execution halted
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by romualdomf0

Hello,

Testing the same as the user in this post is doing could help determine if the database is a factor: C: random error : a possible ram problem?

Please let us know how this results. Thanks, Jen, Galaxy team

ADD REPLYlink written 2.6 years ago by Jennifer Hillman Jackson25k
0
gravatar for romualdomf
2.6 years ago by
romualdomf0
romualdomf0 wrote:

Oh I'm sorry, I forgot to mention. I'm using the usegalaxy.org galaxy server.

ADD COMMENTlink written 2.6 years ago by romualdomf0
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