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Question: What is a "star index" tool dependency?
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gravatar for bisht20diksha
10 months ago by
bisht20diksha • 10
INDIA
bisht20diksha • 10 wrote:

hi- i want to work with rMATS tool that require star indexes. Can anyone please explain me what are these star indexes? As i am unable to understand it properly.
mats rna-seq rna star • 444 views
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modified 10 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by bisht20diksha • 10
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gravatar for Jennifer Hillman Jackson
10 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The star indexes are associated with the tool RNA STAR and are a requirement/dependency for rMATS.

The rMATS tool is not wrapped for Galaxy (at least in the Main Tool Shed http://usegalaxy.org/toolshed). So, I am assuming that you are running this line command.

For help with install, config, and usage, please see the support resources at that tool's development site: http://rnaseq-mats.sourceforge.net/. Or, consider a general bioinformatics forum such as: https://www.biostars.org/.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k

okay. Can we generate star indexes for our genome using RNA STAR at galaxy?

ADD REPLY • link written 10 months ago by bisht20diksha • 10

Indexes can be generated using the RNA STAR Data Manager in your own Galaxy (not on the public servers). These will be linked to the RNA STAR tool, and not others. Even though I don't see why these indexes couldn't be used command-line with other tools, it is the long way to go about generating the data given that the target tool will not be used within Galaxy (rMATS). But you can decide. Thanks! Jen

ADD REPLY • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k
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