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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
407 stars 48 forks source link

Adaptive sampling info #309

Closed nsgarcia27 closed 1 year ago

nsgarcia27 commented 1 year ago

Hello. Is NanoPlot able to generate report on details of an ONT adaptive sampling sequencing run? Specifically want to see if I can get the "Reads completed N50" (for kept reads) and "adaptive sampling voltage reversal N50" (for rejected reads)?

Thanks!

wdecoster commented 1 year ago

That is not currently supported and seems so specific that I probably won't add it. Do you want to start from a sequencing summary file? Is there a column that tells whether the read is completed or rejected?

nsgarcia27 commented 1 year ago

Thanks for the reply. I actually would like to start from the fastq files. There was one sequencing run that got interrupted towards the end and it was not able to generate the summary file. So I was wondering if this tool could regenerate the reports on the barcoded adaptive sampling run.

wdecoster commented 1 year ago

Well, to start I don't know if that information is available in the fastq file, so you'll have to help me understand it here. How do you know for a fastq record/read if the read was completed or rejected?