Question: Filter reads by calculating the distribution of phred score in each individual read
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Nagesh • 10 wrote:
Dear All, I would like to know if there is any tool or script to calculate the distribution of PHRED score for each individual read and filter, if it has the high distribution low quality bases by providing cut-off value. Thanks in advance.
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modified 2.3 years ago
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Devon Ryan ♦ 98k
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2.3 years ago by
Nagesh • 10
You mean a preprocessing tool as FastQC or fastp ?
Try FastQC - https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Is bbduk what you are looking for?
By calculating the average quality, we may miss reads which are having moderate distribution of low quality bases. For example I want to retain reads which are having less than 2% bases with 20 PHRED score.
Fastp has an option for that. BTW, in practice base qualities tend to be fairly bimodal.