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Old 10-23-2013, 10:36 AM   #1
akh22
Junior Member
 
Location: Pittsburgh

Join Date: May 2013
Posts: 7
Default Tophat2 default and custom mapping options

Hi All,

I've been running this tophat2 command, tophat2 -i 20 -I 1200 -g 1 for mapping human RNAseq reads. These numbers are given to me by some others and I am not sure if these settings are appropriate for our application and also if we should stick with default values of Tophat2 rather than using these custom values.

I would very much appreciate if anybody can share values of custom settings of tophat2 for mapping human RNAseq reads.

Thanks in advance.

Aki
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