Processing FASTQ Files

Question

[Carla]

Hello, We have a group project for UMGC it is in accordance with a biotech company that sells electronic notebooks mostly used in bioinformatics. Our main goal is to be able to view Fastq files in the book alongside some metrics that would be of significance. I was wondering what kinds of metrics should we be focusing on viewing alongside the raw data from the fastq file?

Answer 1

[GenoMax]

I was wondering what kinds of metrics should we be focusing on viewing alongside the raw data from the fastq file?

I don't think much can be achieved by viewing raw fastq data. It is plain sequence and encoded Q scores.

FastQC is the de facto standard program used by most for FastQC. Metrics covered in FastQC are what people check.

Your question is unclear. Do you want to implement something like FastQC metrics in the notebook? Please clarify.

[Carla]

Yes, we want to implement some useful metrics if there are any in the notebook.