Question: (Closed) STAR parameters in plants genomes
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gravatar for claudiorivero92
5 months ago by
claudiorivero920 wrote:

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, particularly 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, so I will use it between 60 and 6000 according to what was described for splicing in Arabidopsis, but there are any other parameter that i have to change. Thanks for your attention.

rna-seq star plant • 143 views
ADD COMMENTlink written 5 months ago by claudiorivero920

Hello claudiorivero92!

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ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson23k
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