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Old 08-22-2011, 11:30 AM   #1
vebaev
Senior Res.
 
Location: Plovdiv, Bulgaria

Join Date: Oct 2008
Posts: 110
Default smallRNA GAIIx raw fastq files - quality filter?

Dear all,
I have raw fastq files and I want to do with the help of FASTX toolkit:

1.fastq to fasta
2. clip adaptors
3.collapse to unique sequences

But before that I;m not aware what quality filter to apply to the fastq file in order to remove not quality entries/sequences (probably with fastq_quality_filter sub-program)?

Or if not FASTX do you know what tool to use to make quality filter run and the default option for smallRNA-seq?

Thanks!!!
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