View Full Version : Illumina Very Bad Quality Fastq reads

07-18-2013, 05:35 AM
From your experience, what you do when you have low quality Illumina fastq files (after checked on Fastqc, most parameters are bad),
Do you trim/ filter, but you are going to loose many bases?
Do you mask, I tried this but got vey low mapping quality using BWA?

or should I resequence the strain again?