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Old 04-02-2014, 06:52 AM   #1
Location: Berlin

Join Date: Jul 2013
Posts: 20
Default fastq_quality_filter -p 100 or could be less?

Hello everyone,
I am using FASTX-toolkit to filter my data (small RNA fraction for miRNA analyses) according to quality.
I use the following settings:
fastq_quality_filter -v -q 17 -p 100 -Q 33

This means, that the output will consist in reads where 100% nucleotides are >=17 phred score.

However, when doing that I loss a big amount of reads. For example:
Quality cut-off: 17
Minimum percentage: 100
Input: 95428 reads.
Output: 29635 reads.
discarded 65793 (68%) low-quality reads.

My question is, whether is there a safe trade off between using lower minimum pecentage and still having a good file for mapping.

Thanks in advance
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Old 04-02-2014, 07:01 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Q17 is a pretty strenuous threshold, you might try 5, or better yet just do regular trimming and discard anything too short to map.
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