<p>I need to check which of the predicted de novo transcripts have polyA at 3&#39;. Are polyA tails filtered at some step of tophat/cufflinks processing or this information is retained? If this info is retained, where do I find it. thank you</p>

<p>It&#39;s unclear what TopHat/Cufflinks has to do with the question as you are talking about <em>de novo </em>assembled transcripts. I would just start by using the <strong>grep</strong> command to get a feeling for whether there are any poly-A stretches. It is easy enough to write a script (Perl/Python/whatever) to look for them as well.</p>

<p>Often there are very very few reads with poly-A in HiSeq RNA-seq data, so you might not find much. For some reason there seem to be more poly-A tails left in MiSeq-produced RNA-seq data.</p>
