Hi Haluk,
It is definitely not conventional to remove bases that have low quality,
because this disrupts the DNA sequence and may introduce frameshifts. It
is typically better to trim the ends of the sequence, or to remove it
altogether if its quality does not match your requirements.
Regards,
Hi Florent,
I actually want to do removing respected bases if their quality score is
less than my threshold.
I had been able to do masking those bases by using FASTQ Masker by quality
score tool.
But I haven't gone even one step further for removing bases.
After your reply, I got suspicious. Am I
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
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.
@F4HZV
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