Tophat2 default and custom mapping options

[akh22]

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