How Does Trinity Deal With Polya Tails On Sequencing Reads? Is It Better To Trim Them Of Before Assembly?

Question

[Rahul Sharma]

Hi,

I am running RNA-Seq de-novo assembly, after trimming out Adapter/Primer sequences. I am wondering how does Trinity deal with polyA tails on sequencing reads? Is it better to trim them of before assembly?

Regards

Answer 1

[Istvan Albert]

in general you should perform quality control, trimming and validation yourself rather than expecting tools to implicitly take care of the job.

[Rahul Sharma]

Hi, Thanks for your comment. But I think Trinity is K-mer based de-novo assembler and when it comes across poly-A/T k-mers it will not extend the transcript further. But I am doing Poly-A/T filtering using Prinseq, so will test the difference.

[Istvan Albert]

that does not necessarily sound right, if the polyA is in the middle of the transcript then it is more likely to be valid, if a tool works of kmers then it wouldn't know where that kmer comes from

few things worry me more than "automatic" "smart" decisions that tools make, explicity is always far better than implicit