multiple fastq files - Githubissues

lfrangeu commented 10 months ago

Is it possible to use nanocomp to compar runs if each run contain several fastq.gz files ?

wdecoster commented 10 months ago

No, that is currently not supported. There is some code to do something similar with summary files, but that would require changes for the fastq files.

lfrangeu commented 10 months ago

Thank you for this quick response. I would really like to be able to do this in a future version. Declare folders instead of files for each run in the command line. I'm not a fan of very large files, and I'll have to concatenate all my fastq.gz to be able to use Nanocomp.

-- Lionel Frangeul Viruses and RNAi Institut Pasteur, Université Paris Cité, CNRS UMR3569 25 rue du Dr ROUX, F-75015 Paris, France.

De : Wouter De Coster @.***> Envoyé : jeudi 16 novembre 2023 15:07:47 À : wdecoster/nanocomp Cc : Lionel FRANGEUL; Author Objet : Re: [wdecoster/nanocomp] multiple fastq files (Issue #74)

No, that is currently not supported. There is some code to do something similar with summary files, but that would require changes for the fastq files.

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/wdecoster/nanocomp/issues/74*issuecomment-1814501974__;Iw!!JFdNOqOXpB6UZW0!t4onjXq4hmaWJlCTDl859bLeWzLgk5798YQXlVgU6oQc_5OeXy5-lUpMXuuHZu9-ShD9mU__-TCfCnIgS0XRoMmySJg$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AMC4VD65N4I7U6KQLMDSA6TYEYM3HAVCNFSM6AAAAAA7N7GIV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJUGUYDCOJXGQ__;!!JFdNOqOXpB6UZW0!t4onjXq4hmaWJlCTDl859bLeWzLgk5798YQXlVgU6oQc_5OeXy5-lUpMXuuHZu9-ShD9mU__-TCfCnIgS0XRZkO2OVg$. You are receiving this because you authored the thread.Message ID: @.***>

wdecoster commented 10 months ago

Yes, that makes sense. And you cannot use NanoComp at the summary or BAM/CRAM stage?

wdecoster / nanocomp

multiple fastq files #74