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why multimap is discared from chiA-pet analysis

Hello All I was going through this paper enter link description here

it is said in pet mapping to reference genome paragraph that multimapping tags are discarded for furthur analysis . Can any tell me why this are discarded and why they will select only uniquely mapped reads? Thanks

chia-pet mutplimapped filteration step
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updated by Devon Ryan Devon Ryan • written by Kritika Kritika

1 answer

It's likely that the called interactions would be less reliable if multimappers were included. The alternative would be a two step process where multimappers are first excluded and then included but only if they're concordant with results from the first (no multimapper) iteration. That'd be more time consuming and I'm not sure you'd gain much of anything (I expect someone has tried that).

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written by Devon Ryan Devon Ryan

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