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Question: RNA-STAR Two Pass mode
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gravatar for yelekley7
5 months ago by
yelekley7 • 0
yelekley7 • 0 wrote:

Hello,

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

Thanks
star rna-star rna-seq • 303 views
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modified 5 months ago by Jennifer Hillman Jackson ♦ 25k • written 5 months ago by yelekley7 • 0
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gravatar for Jennifer Hillman Jackson
5 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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

The version at https://usegalaxy.org 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: https://github.com/galaxyproject/usegalaxy-playbook/issues/134

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. https://toolshed.g2.bx.psu.edu/view/iuc/rgrnastar/a70a7eebb435 && https://galaxyproject.github.io/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k
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