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Question: Need help with "Cuffcompare" tool
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gravatar for qiushuhao1985
3.9 years ago by
qiushuhao1985 • 10
United States
qiushuhao1985 • 10 wrote:

Dear Galaxy team,

         Thank you very much for your reply for the last 2 posts. Currently, we get only "=" and "j" class codes with Cuffcompare and Cuffmerge and followed with Cuffdiff analysis. We would like to get an early response for this problem. 

          Thank you!

SQ

 

Tool name: Cuffcompare
Tool version: 0.0.6
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/0.0.6
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/cuffcompare

 
cuffcompare • 907 views
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modified 3.9 years ago • written 3.9 years ago by qiushuhao1985 • 10
1
gravatar for Jennifer Hillman Jackson
3.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is a link to the manual for the different class codes from the tool:
http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/index.html#transfrag-class-codes

I am wondering if you are using a reference annotation dataset with your run? And if so, is it a match for the reference genome? Specifically, the chromosome identifiers must be an exact match.

Some more help for this tool suite is here:
http://wiki.galaxyproject.org/Support see 2.13.2

Best, Jen, Galaxy team
ADD COMMENT • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for qiushuhao1985
3.9 years ago by
qiushuhao1985 • 10
United States
qiushuhao1985 • 10 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?

 

SQ
ADD COMMENT • link written 3.9 years ago by qiushuhao1985 • 10
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