Question: How can I filter RNA-seq reads to remove reads where more than 50% of the read is low quality (Q<20)?
0
gravatar for mar77
3 days ago by
mar770
mar770 wrote:

I'm trying to filter out any reads that consist of more than 50% low quality reads (Q<20). I've already performed filtering steps to remove adapter contamination and remove reads with more than 10% unknown reads, both using cutadapt. Can anyone recommend a tool to use to perform this filtering step? I've previously seen NGSQC Toolkit recommended but I believe this is not supported any longer and I am having trouble accessing it.

Also I am using paired end reads so do these need to be processed together and do I need to use a tool that supports this?

ADD COMMENTlink modified 3 days ago • written 3 days ago by mar770
0
gravatar for Papyrus
3 days ago by
Papyrus210
Papyrus210 wrote:

Assuming you wanted to say " consist of more than 50% low quality bases", I would recommend fastp, it is quite easy to use and has quality filtering options for % of bases within a read not meeting a quality threshold (--unqualified_percent_limit, --qualified_quality_phred should be what you're looking for).

It handles paired-end. Personally I would do all the filtering with the same tool.

(Also, as anticipated by its name, it is quite fast).

ADD COMMENTlink modified 3 days ago • written 3 days ago by Papyrus210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1452 users visited in the last hour