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Question: Need help with "Tophat2" tool
1
gravatar for qiushuhao1985
3.9 years ago by
qiushuhao1985 • 10
United States
qiushuhao1985 • 10 wrote:

Hi Galaxy Team:

           Rice genome has 12 chromosomes. But our output file from Tophat2 is only containing Chr1 to Chr9. We would like to know data alignment for Chr10 to Chr12 is missing.

           We use the same dataset to run Cufflinks and Cuffdiff tools. But we get only "j" and "=" class code. Can you please explain why we are missing rest of the class codes (e.g.: x, o, s, i etc).

Thank you!

 

Tool name: Tophat2
Tool version: 0.6
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/tophat2

 
tophat2 • 788 views
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modified 3.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.9 years ago by qiushuhao1985 • 10
0
gravatar for Jennifer Hillman Jackson
3.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It might be best to start with a sanity check of the inputs. Confirm that your reference genome and reference annotation dataset (if used) contains these chromosomes and that the identifiers are an exact match.

Tools in SAMTool and the Picard groups can help with general statistics beyond what is output by Tophat2. Often clues about content can be discovered this way.

Please let us know if you are still having problems after this, Jen, Galaxy team
ADD COMMENT • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k
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