Wednesday, March 12, 2014

Fwd: thashim / Fixseq — Bitbucket

Found at: (read their full post here)

Fwd: please follow footer link

thashim / Fixseq — Bitbucket: "Overview
FIXSEQ is a over-dispersion correction technique that serves as a smarter way to de-duplicate counts. Consider using FIXSEQ If:
You're going to de-duplicate (remove per base count to one).
Downstream analysis does not account for overdispersion
Downstream analysis is linear (ie SVM or logit regression)
Downsteram analysis uses binned counts
FIXSEQ is not designed for the following use cases:
Correcting exon-level counts (Fixseq will be far too agressive, please use a specialized RNA-seq pipeline)
Correcting nearly single-base spike data such as ChIP-exo (The core assumption of Fixseq is that per-base information can be attenuated safely).
FIXSEQ will most likely not hurt even if your method accounts for overdispersion, but if you already use a specialized analysis pipeline that accounts for overdispersion, there's no need for FIXSEQ.

paper link: PlosCompBio