Hi Haluk, By filtering, you mean removing reads? trimming their ends? or masking some of their bases? There are 3 tools under "Generic FASTQ manipulation" that may help you: Filter FASTQ reads by quality score and length FASTQ Quality Trimmer by sliding window FASTQ Masker by quality score Regards, Florent On 31/07/11 05:58, Haluk Dogan wrote:
Hi,
I am trying to filter my fastq file with the condition of if quality score of reads is less then min score.
So far, I have tried both *fastq_quality_filter* and *Filter FASTQ under NGS: QC and manipulation** *but I was not be able to do it.
In the following you can see my fastq file.
@F4HZV5G02CX6WP rank=0000096 x=1092.0 y=1767.0 length=45 TTGAGCAGCGGCGTCACGGCGGCGGCCTCGGCGGCCGCATAGGCG + FFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIHFFDDBDA>
And these are quality scores. [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 39, 37, 37, 35, 35, 33, 35, 32, 29]
I want to filter bases if their quality scores are less than 33.
Any help would be greatly appreciated.
-- HD
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