Question: View Alignment rate from tophat with illumina
gravatar for christine.nolte
4.0 years ago by
christine.nolte0 wrote:



I guess this is a rather basic and stupid question, but usually I work on Linux and not on Galaxy. I already searched biostar but I couldn't find the answer: How can I view the Alignment rate when using Tophat for Illumina? I get 4 datasets as output, but I kind of miss the summary?



rna-seq • 908 views
ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by christine.nolte0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


There is an open ticket to include the report information for this tool in the output, but as it is the older version, it may not be prioritized. Earlier versions of the Tophap v.1.x wrapper included the report under the "i" info icon's stderr output. However, those are no longer part of the functionality supported on the public Main Galaxy instance and the older wrapper versions may not execute as expected even on a local/cloud.

As an alternative, the Tophat2 tool reports the mapping statistics in the first output dataset created. I would suggest trying this.

Hopefully either Tophat2 will work for you, or you will be able to use the text manipulation/summary tools available in order to generate the statistics you need when using this tool version.

Best, Jen, Galaxy team

ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k
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