Deleting LOW Quality Reads

[AdrianP]

I have a lot of reads for the genome size at hand. My coverage goes above 300 at times.

How do I get rid of reads (with their mates as well) that have NNNN or that have multiple bases at low quality?

For instance let's say I have 28 million pairs of reads and I want top 33% percent that have the highest qualoty (to optimize for 100x coverage)?

Anyone any idea? I seen I can use FastQC to analyse, but not actually remove.

[AdrianP]

bump, I could really use some help. How do I completely get rid of reads that have an overall low quality?

[dpryan]

If you had single-ended reads, then you could just use the fastq_quality_filter function from FASTX-Toolkit. With paired-end reads, I would probably just write a quick little program to filter things. That should be quite simple to do in any programming language and then you can filter however you like.

[JackieBadger]

Take a look at PRINSEQ http://edwards.sdsu.edu/cgi-bin/prinseq/prinseq.cgi
and TRIMMOMATIC http://www.usadellab.org/cms/index.php?page=trimmomatic

[yaximik]

Biopieces have a lot of useful tools and are well documented.