Should I remove duplicates of mapped reads (mr) before using bsrate?

[Ian Chang]

Hi, 

The methpipe manual only mentioned that chromosome names should be sorted before feed mr file to bsrate.

I would like to know if duplicate-remover is required for mapped reads (mr) when using bsrate? 

Thanks.

Ian Chang

[Jianghan Qu]

Hi Ian,

It is better to remove the duplicates before computing the bisulfite conversion rate, otherwise DNA fragments that produced high number of duplicates in the data might bias the bsrate results.

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