Mapping reads on ENCODEBlackListedRegion

Question

[Chirag Nepal]

Hi there,

A lot of CAGE tags map to the encode blacklisted region. I have only mapped the unique reads. I exclude these ~600 regions from downstream analysis. Do you think it is good idea to excluded them at the mapping step. Or is it good to exclude after mapping, so that normalization of tags (to TPM) is done without those reads mapping at blacklisted region.

thanks !

[ATpoint]

Exclude after mapping, then calculate whatever normalization you do on the filtered data.

[Chirag Nepal]

Thank you !! I wanted to confirm.