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Old 03-21-2013, 04:53 AM   #1
Junior Member
Location: Cambridge, UK

Join Date: Apr 2011
Posts: 3
Default Bias adjustment in cufflinks: stranded and unstranded protocol question...

Hello everyone,

I have recently been using the fantastic Cufflinks software package, and had a basic question. A few websites say that bias-adjustment *cannot* be used for unstranded protocols. However, according to the original paper,

"In order to maximize the benefits of bias correction throughout the
RNA-Seq analysis pipeline, we have incorporated it into the Cufflinks
RNA-Seq analysis suite [6], and have pre-configured the software for
specific protocols so that users can reap the benefits of bias correction
for both stranded and unstranded protocols, as well as single- and
paired-end reads. The software is freely available [24] and is distributed
open source under the Boost Software License, version 1.0. "


I know this sounds like a straight forward question, but there are a few online courses saying that bias-adjustment cannot be used for unstranded protocols, which I think is wrong.

Could anyone clarify if you can use the bias-adjustment switch in unstranded protocols?

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