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6.7 years ago
claudiorivero92
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0
Dear all, I want to use the STAR alignment tool available in usegalaxy.org, i know that the default parameters are optimized for mammalian genomes, in my case it's for plant genomes, particulary for legumes. So which parameter i should to change, in my alignment? I know that the intron size is an important issue because the introns in plants are smaller than mammalians, but there are any other parameter that i have to change. Thanks for your attention.
You may wish to post this also on Galaxy Biostars since your question is specific for Galaxy.
If you are able to use a command line then check @Brian's answer here: choosing a suitable max intron size for STAR (plant alignment)