Question: RNA-STAR Two Pass mode
gravatar for yelekley7
5 months ago by
yelekley70 wrote:


I would like to call variants in RNA-seq transcriptome. Is it possible to run RNA-STAR in two-pass mode? If so, how?


star rna-star rna-seq • 303 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by yelekley70
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The version of RNA-STAR at includes --twopassMode when the setting for Other parameters (seed, alignment, limits and chimeric alignment) is set for STAR-Fusion.

The version at is in the middle of an update to fix a bug, and the newer tool version will be installed. Once done, the tool could be used there as well. Details:

Or, you can set up your own Galaxy (local, cloud, docker) and install the most current version from the ToolShed. Update it again once the bug is fixed to capture that correction. &&

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k
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