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afrendeiro / pipelines

[deprecated] Pipelines for ngs
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ATAC-seq specific pipeline #7

Closed afrendeiro closed 9 years ago

afrendeiro commented 9 years ago

Fragments up to 2 kb allowed to align (-X2000) and only unique aligning reads were collected (-m1)

Reads aligning to the + strand offset by +4 bp, and reads aligning to the – strand offset −5 bp.

Call peaks with Zinba:

"ZINBA was run using a window size of 300 bp and an offset of 75 bp. Alignability was used to model the zero-inflated component, and the ATAC- seq read count for the background and enriched components. Enriched regions were identified as those with a posterior probability of >0.8" \cite{Buenrostro2013}

afrendeiro commented 9 years ago

Implemented in 891e3821bb857b0b6fff6bfa98fc2af796ecd45a