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schatzlab / genomescope

Fast genome analysis from unassembled short reads
Apache License 2.0
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question about genome size #35

Open tiramisutes opened 4 years ago

tiramisutes commented 4 years ago

Hi, The estimated genome size of the coastal redwood output by GenomeScope is 27.0 Gbp and 2.293 Gbp for Gossypium barbadense in this paper <GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes>. But I'm confused about how to get these results from http://qb.cshl.edu/genomescope/genomescope2.0/analysis.php?code=example7 and http://qb.cshl.edu/genomescope/genomescope2.0/analysis.php?code=example8 website?

tbenavi1 commented 4 years ago

Hello, GenomeScope reports the genome size for a single chromosome set. Since Gossypium barbadense is a tetraploid species, we multiply 572,773,156 by 4 to get 2,291,092,624. For the coastal redwood, the data come from a megagametophyte and thus the data is triploid. When we multiply 8,953,695,151 by 3, we get 26,861,085,453 as expected.

tiramisutes commented 4 years ago

So, is the Genome Haploid Length the final genome size of a diploid species?

mschatz commented 4 years ago

For the human genome, GenomeScope would report 3Gb (the haploid genome) while the total DNA content per cell is about 6Gb (the diploid genome size). Hope this helps!

Mike

tiramisutes commented 3 years ago

For an autohexaploid genome, should we set the Ploidy to six in genomescope2.0 and finally genome size equal multiply Genome Haploid Length by 6？ 20200923224642

mschatz commented 3 years ago

Yes, thats it

On Wed, Sep 23, 2020 at 10:52 AM hope notifications@github.com wrote:

For an autohexaploid genome, should we set the Ploidy to six in genomescope2.0 and finally genome size equal multiply Genome Haploid Length by 6？ [image: 20200923224642] https://user-images.githubusercontent.com/10768210/94028786-c2c5ad00-fdee-11ea-9c33-15ef83ac9350.png

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tiramisutes commented 3 years ago

I'm a little confused. For cotton genome

For an autohexaploid genome, should we set the Ploidy to six in genomescope2.0 and finally genome size equal multiply Genome Haploid Length by 6？ 20200923224642

So, the final genome size equal multiply Genome Haploid Length by 6. This is a single chromosome set (haploid of three sets of chromosomes) or six sets of chromosomes? I'm a little confused. Because for the Gossypium barbadense, genome size 2,291,092,624 is a size of single chromosome set. but still multiply by 4.