how to filter overlap MAF

[Zheng Yan]

Hi Maffilter,

I am try to do alignment between two genome, but both are scaffold. And after filter with low score than 500, the result is still have a lot of region where different query align to some reference region. Would you please let me know if Maffilter can remove the redundant alignment region?

many thanks,

Yan  

[Julien Yann Dutheil]

Dear Yan,

You can do that using the Subset filter, it has a remove_duplicates option (http://biopp.univ-montp2.fr/manual/html/maffilter/v1.1.0/Subset.html#Subset). By doing so, all regions where a species does not map uniquely will be filtered out.

Hope this helps,

Julien.