<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>Most reads from bridge amplification wouldn&#39;t contain polyA&#39;s nor would they ever make it past alignment. I think you are confusing de novo transcriptome assembly with ab initio isoform discovery.</p>
