Question: What to do with Cuffquant .cxb files
gravatar for henrikad
3.2 years ago by
United States
henrikad0 wrote:

I would like to get a raw RNA-Seq counts matrix from the results of the Tophat alignment to a reference genome. Figured Cuffquant would do the trick, but what to do with the .cxb file that results?? Why not a .csv file, or at least the option to pick up front? Any suggestions anyone? 

BTW, it would be lovely if it were possible to access htseq from the Galaxy menu and input BAM files and the gtf and get a raw counts matrix out.


ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by henrikad0
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Use Cuffnorm to obtain a final tabular result file. Cuffquant is performing a portion of the calculations needed for this type of summary, but not all. Also see the Release Notes and Manual for more help.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k


Cuffnorm normalizes the counts, albeit in a variety of methods, but still the output is still normalized.  I need raw counts for DESeq2 input.  All I want are the alignment counts.  Would be nice if HTSEQ was a part of the Galaxy tools.


ADD REPLYlink written 3.2 years ago by henrikad0
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