Discard reads with low quality

Question

[K.Nijbroek]

Hi,

I've got Illumina Paired-End reads (2x 150 in --fr orientation). I want to filter my .SAM/.BAM files based on average read quality. Does anyone know an easy to use tool (Preferable which can run via Java or Windows), which is able to discard reads when average quality is <20?

Answer 1

[Ashutosh Pandey]

BBMap is a tools that can be used to discard reads from SAM files with average quality less than some threshold. Additionally, it can be used to trim bad quality 3' ends of the reads within the SAM file. BTW, it is always advisable to carry base quality filtering operations at the fastq level rather than aligned read (SAM or BAM) level.

See links below:

• http://sourceforge.net/projects/bbmap/
• http://seqanswers.com/forums/showthread.php?t=41057
• http://seqanswers.com/forums/showthread.php?t=42268

[Phil S.]

without checking the seqanswers links you can also go with trimmomatic or cutadapt for filter the fastq files before mapping (which also makes sense in terms of CPU-time....