Question: Need help with "Cuffcompare" tool
gravatar for qiushuhao1985
3.9 years ago by
United States
qiushuhao198510 wrote:

Dear Jennifer,

          We did not get the right information what we are looking for. The only class codes after Cuffcompare and Cuffmerge we get is "=" and "j". Other Class codes which are "o", "i", "s", "x" are missing after analysis. Can you please let us know if Cufflinks from Galaxy only selects the class code is "=" and "j" and not others?




Tool name: Cuffcompare
Tool version: 0.0.6
Tool ID:
ToolShed URL:


cuffcompare • 790 views
ADD COMMENTlink modified 3.9 years ago by Jennifer Hillman Jackson25k • written 3.9 years ago by qiushuhao198510
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


I see that you posted twice for this, but will reply here.

We didn't get feedback about whether you are using a reference annotation dataset? Many of these codes are dependent on that information, as described in the manual.

If you are using one, then confirming that the data are an exact match is critical (specifically the chromosome identifiers between the reference genome and the GTF/GFF3 dataset in use). Otherwise, the annotation will be ignored, and certain classes cannot be assigned.

It seems that you are installing locally now, so perhaps that will help, as you will have full control over the inputs that way.

Thanks, Jen, Galaxy team


ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k
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