search

a-slide / pycoQC

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
https://a-slide.github.io/pycoQC/
GNU General Public License v3.0
271 stars 41 forks source link

Info barcode analysis #148

Open KristinaGagalova opened 10 months ago

KristinaGagalova commented 10 months ago

Hi,

Thank you for working on such a great tool for ONT analysis.

I have a question on the possible analysis that can be performed on barcoded reads. In particular, I am interested to know if we could use pycoQC for the comparison of different barcoded samples. I have two treatments with barcodes and I was wondering if there is a comparison that can be done. The summary file considers the entire set of reads generated by a run but can be that broken down to the barcode level?

Any suggestion or input is appreciated

KristinaGagalova commented 10 months ago

I just found the --barcode-file option where you can add a barcode list. Do you maybe have an example of that?

In the documentation you mention

--barcode_file [BARCODE_FILE ...], -b [BARCODE_FILE ...]
                        Path to the barcode_file generated by Guppy 2.1.3+ (guppy_barcoder) or Deepbinner
                        0.2.0+. This is not a required file. One can also pass multiple space separated file
                        paths or a UNIX style regex matching multiple files (optional)

Can you please explain "One can also pass multiple space separated file paths or a UNIX style regex matching multiple files"

What are the file paths? To the fatsq files?

SMWakeman commented 9 months ago

Jumping in on this too, what file is the 'barcode file' specified here? As I'd really like to get this working for QC'ing my barcoded runs