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theaidenlab / AGWG-merge

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Juicer which parameters? #3

Open matryoskina opened 4 years ago

matryoskina commented 4 years ago

Hello! I am wondering if you run Juicer to produce the duplicate-free list of paired alignment with default parameters, or if you went for more stringent alignment parameters, like "only perfect matches", to facilitate the 3D pipeline analysis.

Best

dudcha commented 4 years ago

Hello,

For 3D-DNA Juicer is typically run with default parameters (see Genome Assembly Cookbook for more details on dnazoo.org/methods). Note that for diploid the maps are built with mapq0 reads as described below).

Best, Olga

On Sep 22, 2020, at 8:54 AM, matryoskina notifications@github.com wrote:

 Hello! I am wondering if you run Juicer to produce the duplicate-free list of paired alignment with default parameters, or if you went for more stringent alignment parameters, like "only perfect matches", to facilitate the 3D pipeline analysis.

Best

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