Question: Filter reads by calculating the distribution of phred score in each individual read
0
gravatar for Nagesh
2.3 years ago by
Nagesh10
IN
Nagesh10 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.

sequencing rna-seq next-gen • 837 views
ADD COMMENTlink modified 2.3 years ago by Devon Ryan98k • written 2.3 years ago by Nagesh10
1

You mean a preprocessing tool as FastQC or fastp ?

ADD REPLYlink written 2.3 years ago by Bastien Hervé4.9k

Try FastQC - https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

ADD REPLYlink written 2.3 years ago by Sej Modha4.7k

Is bbduk what you are looking for?

bbduk.sh in=reads.fq out=clean.fq maq=10

This will discard reads with average quality below 10. If quality-trimming is enabled, the average quality will be calculated on the trimmed read.
ADD REPLYlink written 2.3 years ago by finswimmer14k

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.

ADD REPLYlink written 2.3 years ago by Nagesh10

Fastp has an option for that. BTW, in practice base qualities tend to be fairly bimodal.

ADD REPLYlink written 2.3 years ago by Devon Ryan98k
0
gravatar for Devon Ryan
2.3 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

As mentioned in the comments, bbduk and fastp can both do this.

ADD COMMENTlink written 2.3 years ago by Devon Ryan98k
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