Question: Adapter for RNA-seq alignment
0
gravatar for chjiao3456
6.1 years ago by
chjiao345640
Michigan State University, USA
chjiao345640 wrote:

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.

rna-seq alignment • 3.2k views
ADD COMMENTlink modified 6.1 years ago by iraun3.8k • written 6.1 years ago by chjiao345640
1
gravatar for Devon Ryan
6.1 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

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).

ADD COMMENTlink written 6.1 years ago by Devon Ryan97k

Thanks, which trim tool would you suggest?

ADD REPLYlink written 6.1 years ago by chjiao345640

There are two popular ones cutadapt and fastx clipper

I would go for cutadapt, 

ADD REPLYlink written 6.1 years ago by Manvendra Singh2.1k

Thanks, cuadapt is a good tool.

ADD REPLYlink written 6.1 years ago by chjiao345640
1
gravatar for iraun
6.1 years ago by
iraun3.8k
Norway
iraun3.8k wrote:

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 (http://www.usadellab.org/cms/?page=trimmomatic), which can deal with both Paired-End (PE) and Single-End (SE) data.

ADD COMMENTlink written 6.1 years ago by iraun3.8k

Thanks for your recommendation.

ADD REPLYlink written 6.1 years ago by chjiao345640
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