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Old 07-18-2013, 05:35 AM   #1
mmmm
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Location: UK

Join Date: Jul 2013
Posts: 131
Default Illumina Very Bad Quality Fastq reads

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?
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