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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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Detailed explanation of snaptools preprocessing parameters #71

Open emrecaglayan opened 5 years ago

emrecaglayan commented 5 years ago

I couldn't find a manual page of some sort that explains every parameter being used in snaptools. Some of them are explained in: https://github.com/r3fang/SnapATAC/wiki/FAQs But some are not clearly written.

For example, in snaptools snap-pre what does --max-num=20000 exactly do? Does it take the top 20k cells with the most cell barcodes?

r3fang commented 5 years ago

Sorry for not documenting it clearly. --max-num=20000 means it take the top 20k cells with the most reads

-- Rongxin Fang, Ren Lab Ludwig Cancer Research Bioinformatics Ph.D. Student University of California, San Diego

On Aug 23, 2019, at 10:11 AM, emrecaglayan notifications@github.com wrote:

I couldn't find a manual page of some sort that explains every parameter being used in snaptools. Some of them are explained in: https://github.com/r3fang/SnapATAC/wiki/FAQs https://github.com/r3fang/SnapATAC/wiki/FAQs But some are not clearly written.

For example, in snaptools snap-pre what does --max-num=20000 exactly do? Does it take the top 20k cells with the most cell barcodes?

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