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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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custom genome #106

Closed BingbingYuan closed 4 years ago

BingbingYuan commented 4 years ago

Can snapATAC deal with custom genome? Based on the description of snaptools snap-pre (below), I think I can just use any genome build. But, I'm concerning what would be happened when I combine two samples later on. I have two samples, each from different developmental stage. Could you explain a bit more on "This tag does not change anything unless merge or compare multiple snap files"

--genome-name GENOME_NAME genome identifier (i.e. hg19, mm10). This tag does not change anything unless merge or compare multiple snap files. (default: None) Thanks,

r3fang commented 4 years ago

Hi you can totally ignore this tag, it is not used in the downstream analysis

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On Sep 26, 2019, at 2:27 PM, BingbingYuan notifications@github.com wrote:

Can snapATAC deal with custom genome? Based on the description of snaptools snap-pre (below), I think I can just use any genome build. But, I'm concerning what would be happened when I combine two samples later on. I have two samples, each from different developmental stage. Could you explain a bit more on "This tag does not change anything unless merge or compare multiple snap files"

--genome-name GENOME_NAME genome identifier (i.e. hg19, mm10). This tag does not change anything unless merge or compare multiple snap files. (default: None) Thanks,

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