Re: [Transdecoder-users] Does TranscriptDecoder also predict polyA?

[Trakhtenberg, F. <Eph...@ch...>]

Thank you for the clarification. Any recommendations on which tool I could use for predicting polyA?



________________________________
From: Brian Haas [bh...@br...]
Sent: Saturday, July 19, 2014 5:53 PM
To: Trakhtenberg, Feliks
Cc: tra...@li...
Subject: Re: [Transdecoder-users] Does TranscriptDecoder also predict polyA?

Hi,

TransDecoder does not take into account whether a transcript is polyadenylated or not. It strictly looks at open reading frames and coding potential.

best,

~brian



On Sat, Jul 19, 2014 at 2:38 PM, Trakhtenberg, Feliks <Eph...@ch...<mailto:Eph...@ch...>> wrote:
Hello, I am new to TranscriptDecoder. Does it consider whether a novel transcript with a predicted ORF is also predicted to be polyadenylated? I assumed if no polyA can be predicted, then even if ORF is predicted, such transcript may not produce a protein. My input is a group of novel transcripts predicted by Cufflinks analysis. Would appreciate feedback. thank you

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Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas