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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