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ajlabuc / meCLIP

Snakemake based analysis pipeline to identify m6As from eCLIP data
MIT License
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Can we use customized genome ? #1

Closed LoneKnightz closed 1 year ago

LoneKnightz commented 1 year ago

Hi,

Thanks for providing this powerful tools for m6a.

I have checked your document and it seems we can only download the genome for this pipeline.

May I ask can I use our own genome and gif?

Should I just change the url to our genome path in manual-reference-genome.yml ?

Or is there any way to do that?

Thanks

NanoCoreUSA commented 1 year ago

Hi @LoneKnightz,

Apologies for the late reply, I must have missed the notification.

Yes, I've recently made some updates to the pipeline and you should be able to input custom genomes using the 'manual-reference-genome.yml' file and then executing the command below.

snakemake --snakefile workflow/rules/genome-download.smk --cores N

Please let me know how it goes, I haven't gotten a chance to test this feature much so would be curious how it works.

LoneKnightz commented 1 year ago

Thanks!