Adapter for RNA-seq alignment

Question

[chjiao3456]

Hi everyone:

I'm not quite familiar with RNA-seq alignment. It seems that part of the RNA-seq reads (splice site) can be mapped to reference genome by alignment tool Tophat or STAR. In this case, do we need to remove the adapters for sequencing reads with tools like cutadapt? For small RNA-seq, since the sequencing reads length is increasing, there is high possibility that the reads will contain adapter sequences.

Answer 1

[Devon Ryan]

It's always a good idea to trim off the adapters (note that if you have paired-end reads, only use a trimmer that trims as a pair). You can also quality trim, but don't do that aggressively (certainly don't go over a minimum Phred score of 5).

[chjiao3456]

Thanks, which trim tool would you suggest?

[Manvendra Singh]

There are two popular ones cutadapt and fastx clipper

I would go for cutadapt,

[chjiao3456]

Thanks, cutadapt is a good tool.

Answer 2

[iraun]

The presence of adapter sequences in your reads can affect dramaticaly the % of the alignment and also the quality. So, as Devon said, it's always a good practice to remove them. I suggest you to use Trimmomatic, which can deal with both Paired-End (PE) and Single-End (SE) data.

[chjiao3456]

Thanks for your recommendation.