Question: RNA-STAR Two Pass mode
0
gravatar for yelekley7
10 weeks ago by
yelekley70
yelekley70 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 • 137 views
ADD COMMENTlink modified 10 weeks ago by Jennifer Hillman Jackson25k • written 10 weeks ago by yelekley70
0
gravatar for Jennifer Hillman Jackson
10 weeks ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 10 weeks ago by Jennifer Hillman Jackson25k
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