How to deal with adapter dimers?

Question

[BioinfoNovice]

Hi guys,

I'm checking my raw reads that I have freshly obtained. I saw the presence of adapter sequences not only on the 3' end but also on the 5' end and sometimes in the middle of reads. After some discussions and research, it seems that I have some adapter dimers in my raw reads.

Knowing that, I would like to apply tools that trim adapters. I wanted to use Trim Galore but it seems that it only remove adapters at the 3' end. Am I wrong? Otherwise, what are tools that could handle the presence of adapters on the 5' end?

Do cutadapt and Trimmomatic only deal with adapters on the 3' end also?

I'm still not familiar with all the tools out there. So, your answers could be really helpful. Thank you very much in advance.

Answer 1

[dariober]

trim_galore is a wrapper around cutadapt. Cutadapt has several options to tune the trimming, including 3', 5', middle of the read.

Answer 2

[Gabriel R.]

I think you are describing chimeric reads. We published a study about leeHom, our algorithm for adapter removal which enables the possibility of flagging chimeric reads and removing them from downstream analysis:

paper:

http://www.ncbi.nlm.nih.gov/pubmed/25100869

software:

http://grenaud.github.io/leeHom/

Hope this helps!

[BioinfoNovice]

That seems interesting ! I will take a look on it although I've already managed to use trim_galore to trim my data. Thanks.