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davidaknowles / leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
http://davidaknowles.github.io/leafcutter/
Apache License 2.0
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LeafCutter Intron Clustering Time #262

Open ronv-fishers opened 2 weeks ago

ronv-fishers commented 2 weeks ago

Hello,

I'm analyzing RNA sequencing data of samples from every chromosome, and I'm trying to gauge the expected duration for the Intron Clustering process. In my recent analysis, processing 10 samples took approximately 62 seconds using 2 CPU cores and 7 GB of memory, and I was wondering if this seems reasonable? I thought this would be too quick, for reference, juncing took 50 minutes for 10 samples.

Thank you for your time.

jackhump commented 2 weeks ago

clustering is very fast - we regularly do it on 100s of samples in a few minutes. Junction extraction is much slower.