How can I get PHRED score?

Question

[Riku]

Hi, all.

I am trying to get the assembly stat(Table S1.) according to the following paper about de novo assembly.

[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7266049/][1]

In the table, there is an item "Mean read PHRED score after filtering and trimming”. How can I get this?

Is there any way I can calculate the PHRED score based on the fasta file?

I really appreciate your time and effort!

[MK]

Is there any way I can calculate the PHRED score based on the fasta file?

You would need fastq files.

You can use FastQC to check the quality of your reads and then create report with MultiQC. It is possible to download a phred scores for all samples from MultiQC in csv or JSON format.

[Riku]

Sorry for not responding sooner.

Thanks to you, I was able to get PHRED score with multiqc. It was very easy to just run multiqc in the directory where the fastqc resulats are.

Your advices was very helpful for me. I really apreciate your help!

Answer 1

[MSRS]

Is there any way I can calculate the PHRED score based on the fasta file?

No, Phred quality score data can be found in .abI file in sangar/capillary sequencing data or in Fastq/bam file in NGS data.

[Riku]

Thank you very much for your advices! It seems that I have to check fastq file.