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RNA STAR parameters in Galaxy project

Hi everyone!

I am new to Biostars and would love some help with understanding the BAM output format specifications under RNA STAR on usegalaxy.org

I have uploaded my Illumina MiSeq bulk RNA-seq dataset to Galaxy and am now ready to align it to the human genome (I have sequenced human cancer cells) using RNA STAR.

I can't find any information online or on Galaxy to explain what each of the following tickboxes mean when choosing parameters for your BAM output specs. Please could someone shed some light on these? I would be most grateful!

Thank you :)

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galaxy rna-seq star
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updated by Ram Ram • written by marianne_best • marianne_best

1 answer

Check out the STAR Manual. Specifically section 5.2.2. This galaxy tool is just a wrapper around this command line tool so it is often best to go straight to the original docs.

The outputs you need may depend on what downstream analysis you are running. If you have any ones in particular you want to know about just ask.

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written by Jack Tierney • Jack Tierney

Amazing thank you! I will check that out now :)

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written by marianne_best • marianne_best

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