Does anyone have experience using findtail?

Question

[pubsurfted]

My professor wanted me to remove poly a tails from the rna seq data because he said internal priming could skew the end results. I asked him to provide me with a tool to do that and he gave me this link:

https://code.google.com/archive/p/findtail/downloads

The link only contains the downloadable file of the program findtail and nothing else. I couldn't find any description of how to use it.

I was hoping anyone here could provide me with any insight.

Answer 1

[shelkmike]

I have never used Findtail, but you can trim poly-A tails with Cutadapt, see https://cutadapt.readthedocs.io/en/stable/recipes.html#trim-poly-a-tails

Answer 2

[benformatics]

I am sorted of confused by the use of the word internal priming. Usually that means that sequence adjacent to homopolymer-tracts of A within mRNA will become enriched due to the polyA-based random priming (used for example in mainstream RNA-seq library preps). So you will have reads enriched in sites that are relatively far from the polyA tail. To remove these you need to identify them genome-wide.

Trimming polyA-tails is not super necessary for aligners that do softclipping but otherwise you can use a trimming tool like the one suggested by @sheikmike