Comments (7)
mschatz
commented on August 13, 2024
This is one of those challenging situations where it is ambiguous if it is
a larger haploid genome with low heterozygosity (v1, 463Mb @ .113%
heterozygosity) versus a smaller haploid genome with very
high heterozygosity (v2, 251Mb @ 16.1% heterozygosity) Do you know anything
about the genetic architecture of this? My blind guess is the v1 model is
probably accurate since 16.1% heterozygosity would be extremely high from a
single individual. You can help inform the genomescope 2.0 model to give a
very similar result by giving it a hint that the "Average k-mer coverage
for polyploid genome" to be 114.
Good luck!
Mike
…On Fri, Dec 11, 2020 at 8:25 AM Patrick Tran Van ***@***.***> wrote:
Hi,
I used genomescope from this repo:
https://github.com/schatzlab/genomescope
and
https://github.com/tbenavi1/genomescope2.0
And got weird results:
From v1:
https://ibb.co/FXPYPgV
From v2:
https://ibb.co/XC7Y5Nx
What could explain those big differences ?
hist have been generated with:
kmc -k21 -t5 -m64 -ci1 -cs10000 @cat.files cat.kmcdb tmp
kmc_tools transform cat.kmcdb histogram cat.kmcdb_k21.hist -cx10000
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ptranvan
commented on August 13, 2024
Hello, we don't know many things about the genomic architecture of this species but it should be diploid. I did change "Average k-mer coverage "for polyploid genome" to 114 but got the same plot:
GenomeScope version 2.0
input file = user_uploads/va4PdkFoOZtVXygmISbA
output directory = user_data/va4PdkFoOZtVXygmISbA
p = 2
k = 21
initial kmercov estimate = 114
property min max
Homozygous (aa) 0% 100%
Heterozygous (ab) 0% 100%
Genome Haploid Length 251,713,776 bp 251,965,450 bp
Genome Repeat Length 52,929,734 bp 52,982,656 bp
Genome Unique Length 198,784,041 bp 198,982,794 bp
Model Fit 79.394% 92.8582%
Read Error Rate 0.236534% 0.236534%
http://genomescope.org/genomescope2.0/analysis.php?code=va4PdkFoOZtVXygmISbA
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mschatz
commented on August 13, 2024
Sorry, I should have said run it setting the average coverage to by 57 so
that it will realize the tall peak at 117x is the homozygous kmer peak:
http://qb.cshl.edu/genomescope/genomescope2.0/analysis.php?code=W2E0vPLDTdDqDT038A18
Cheers
Mike
…On Mon, Dec 14, 2020 at 5:51 AM Patrick Tran Van ***@***.***> wrote:
Hello, we don't know many things about the genomic architecture of this
species. I did change "Average k-mer coverage "for polyploid genome" to 114
but got the same plot:
GenomeScope version 2.0
input file = user_uploads/va4PdkFoOZtVXygmISbA
output directory = user_data/va4PdkFoOZtVXygmISbA
p = 2
k = 21
initial kmercov estimate = 114
property min max
Homozygous (aa) 0% 100%
Heterozygous (ab) 0% 100%
Genome Haploid Length 251,713,776 bp 251,965,450 bp
Genome Repeat Length 52,929,734 bp 52,982,656 bp
Genome Unique Length 198,784,041 bp 198,982,794 bp
Model Fit 79.394% 92.8582%
Read Error Rate 0.236534% 0.236534%
http://genomescope.org/genomescope2.0/analysis.php?code=va4PdkFoOZtVXygmISbA
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ViriatoII
commented on August 13, 2024
I'm also curious about this. Genomescope1 seems to have estimations in line with literature for my species while genomescope2 not (even when multiplying by 2 because of haploid vs diploid)
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mschatz
commented on August 13, 2024
Thats the usual issue. If you post the links to the results I can give more
specific comments.
Cheers
Mike
…On Thu, Aug 19, 2021 at 7:31 AM ViriatoII ***@***.***> wrote:
I'm also curious about this. Genomescope1 seems to have estimations in
line with literature for my species while genomescope2 not (even when
multiplying by 2 because of haploid vs diploid)
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ViriatoII
commented on August 13, 2024
Hi Mike,
That's very kind of you, thank you.
As an example, this D. erucoides is estimated to have ~500 Mbps haploid genome size, 1000 Mbps in diploid size ( Lysák et al.,2009)
Genomescope1 predicts 435 Mbps haploid length, just short of literature, as well as a reasonable 0.65% of heterozygosity:
http://qb.cshl.edu/genomescope/analysis.php?code=izm95ZeGs1WxSvj8bidT
The genomescope2 run (even using max 100 000 coverage) predicts 212Mbps of haploid genome length, and a surprising max estimated heterozygosity of 20%.
http://qb.cshl.edu/genomescope/genomescope2.0/analysis.php?code=cKhv8wWNKBHMEgf3ilHd
I am applying the same pipeline to 20 species, some of which are tetraploid. I'd wish I could just apply the same parameters to all, or at least only treat the tetraploids differently and give them to genomescope2.
Appreciate the help,
Ricardo
from genomescope.
mschatz
commented on August 13, 2024
Hi Ricardo
It looks like GenomeScope2 got a little confused on which peak was which -
notice in GS1 the first peak (kcov) is at 19, but in GS2 the first peak is
at 38. In these cases, you can give the algorithm a hint as to which peak
should be the first peak. On the website it is listed as "Average k-mer
coverage for polyploid genome". If I give it at hint of 19, the GS2 results
are very similar to the GS1 results:
http://qb.cshl.edu/genomescope/genomescope2.0/analysis.php?code=2PR3qCNoIXJQ22mXMC6d
Looking at this I think GS2 gets confused by the excess of kmers that have
a coverage around 10-20 that dont look like normal sequencing errors. I
would guess your sample has a somewhat unusual structure, such as some
contamination or maybe unbalanced representation of sex chromosomes. It
also looks like the genome size estimate is smaller than expected because
the kmer distribution is truncated at 10000x coverage. If you increase this
to 100,000 or 1,000,000 it will capture more of the higher order repeats
and increase the genome size.
Good luck!
Mike
…On Fri, Aug 20, 2021 at 4:37 AM ViriatoII ***@***.***> wrote:
Hi Mike,
That's very kind of you, thank you.
As an example, this D. erucoides is estimated to have ~500 Mbps *haploid*
genome size, 1000 Mbps in diploid size ( Lysák et al.,2009)
Genomescope1 predicts 435 Mbps *haploid* length, just short of
literature, as well as a reasonable 0.65% of heterozygosity:
http://qb.cshl.edu/genomescope/analysis.php?code=izm95ZeGs1WxSvj8bidT
The genomescope2 run (even using max 100 000 coverage) predicts 212Mbps of
haploid genome length, and a surprising max estimated heterozygosity of 20%.
http://qb.cshl.edu/genomescope/genomescope2.0/analysis.php?code=cKhv8wWNKBHMEgf3ilHd
Appreciate the help,
Ricardo
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Related Issues (20)
- smaller genome size and lower heterozygosity
- potentially poor fitting model for proposed tetraploid HOT 1
- FAQ not up to date regarding ploidy HOT 1
- No file uploaded error message HOT 3
- Low model fit while ran Genomescope 2.0
- Strange genomescope result HOT 1
- High heterozygous? HOT 3
- No file upload message HOT 1
- Unable to converge HOT 3
- 503 Service Unavailable HOT 2
- mergeing HiFi data of two samples didn't increase hetorozygosity
- Heterozygosity rate < 0 HOT 3
- expectations for pooled samples HOT 2
- Heterozygous tetraploid genome model fit HOT 2
- GenomeScope Output from PacBio Hifi ccs Reads is Confounding HOT 3
- Model and observations don't converge HOT 3
- dup (in figure) and bias (in model.txt) HOT 2
- Follow up RE: Confounding GenomeScope Output HOT 5
- Ploidy determination HOT 1
- Heterozygous peak identified as errors? HOT 3
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