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  • akh22
    Junior Member
    • May 2013
    • 7
    #1

    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
    Tags: None
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