Comments (5)
mschatz
commented on August 13, 2024
This shows the genome is about 3Mbp in size and about 98% unique (2%
repetitive), and with very low heterozygosity. Is this a microbial genome?
Good luck
Mike
…On Mon, Oct 21, 2019 at 5:19 PM Dimpal1989 ***@***.***> wrote:
Hello Sir,
I hope you are doing well.
I am trying to use genome scope in order to know the percentage repeat
content of the genome. I am having a hard time understanding the output.
Can you please please help me out with this. The results I obtained are
attached below. How can the interpret further that this much percentage of
my genome is having repeat content by looking at results?
I ran the following command in order to get the results.
1.
download jellyfish:
wget
https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz
2.
untar the file
tar -xvzf jellyfish-2.3.0.tar.gz
3.
download the linux one too.
wget
https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-linux
4.
went to the jellyfish directory.
cd jellyfish-2.3.0/
5.
ran count to find kmers:
./bin/jellyfish count - C -m 21 -s 1000000000 -t 10 *.sra.fasta -o
reads.jf
6.make histo file and dragged it to the site.
./jellyfish-2.3.0/bin/jellyfish histo -t 10 reads.jf > reads.histo
[image: Screenshot (154)]
<https://user-images.githubusercontent.com/53311834/67243938-5001c400-f41e-11e9-998b-594dc14c5cb9.png>
[image: Screenshot (155)]
<https://user-images.githubusercontent.com/53311834/67243939-5001c400-f41e-11e9-8a96-d0c426280a05.png>
[image: Screenshot (156)]
<https://user-images.githubusercontent.com/53311834/67243940-5001c400-f41e-11e9-8b39-f6044c947985.png>
Your suggestion will really helpful.
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dlata123
commented on August 13, 2024
Thank you so much for the prompt reply. Yes, this belongs to Listeria Monocytogenes.
a) if I got you correct you came up with those numbers [(98% unique (2%
repetitive) and with very low heterozygosity)], based on the genome haploid length which is 3032448 bp. Next in order to see a repetitive content percentage, we divide 34907 / 3032448 bp which is approx 2% and while the unique one is 2997541/3032448 = approx 98%. Am I correct here ?????
b) The plot which we get here : Genome scope profile. The only difference which I can see in both of them is the second one has coverage threshold? what is the significance, and usage of these two plots, how are they different? Moreover, these two plot gives these number [ dup: 1.59%, unique: 98.8 %, kcov: 17.4, error:1.1%] what does kcov imply, The mean of these plots are even different. how can we say that the plot is giving correct value, how are plot interpreted?
c) The genome scope can be used to analyze repeat content for a larger eukaryotic genome size even like humans for example. Just that we will need to adjust the kmer number based on it. Am I right??
Thanks for the help. I really appreciate it.
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mschatz
commented on August 13, 2024
On Mon, Oct 21, 2019 at 10:08 PM Dimpal1989 ***@***.***> wrote:
Thank you so much for the prompt reply. Yes, this belongs to Listeria
Monocytogenes.
a) if I got you correct you came up with those numbers [(98% unique (2%
repetitive) and with very low heterozygosity)], based on the genome
haploid length which is 3032448 bp. Next in order to see a repetitive
content percentage, we divide 34907 / 3032448 bp which is approx 2% and
while the unique one is 2997541/3032448 = approx 98%. Am I correct here
?????
Yes, thats right.
b) The plot which we get here : Genome scope profile. The only difference
which I can see in both of them is the second one has coverage threshold?
what is the significance, and usage of these two plots, how are they
different? Moreover, these two plot gives these number [ dup: 1.59%,
unique: 98.8 %, kcov: 17.4, error:1.1%] what does kcov imply, The mean of
these plots are even different. how can we say that the plot is giving
correct value, how are plot interpreted?
The second plot uses a log scale, but since this is a bacteria, there arent
many high copy repeats so they look similar. They look very different for
larger genomes, such as the example plot for Arabidopsis:
http://qb.cshl.edu/genomescope/analysis.php?code=example6
c) The genome scope can be used to analyze repeat content for a larger
eukaryotic genome size even like humans for example. Just that we will need
to adjust the kmer number based on it. Am I right??
Yes, it works well for larger genomes too
Good luck
Mike
… Thanks for the help. I really appreciate it.
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dlata123
commented on August 13, 2024
Thanks for responding back, I wanted to confirm one more thing, I want to use the Genome Scope approach in order to see the percentage of repetitive elements in a genus of beetle, which has a genome size close to the human being. In that scenario should I use a range of kmers size, and see by using which size of kmer will give me minimum error rate, and choose that particular kmer value to interpret the repetitive content of the genome. ???? This is just a thought because I read somewhere for a larger genome, it good change kmer size.
Is there any place where I can read about the plots generated by the genome_scope?? Lastly from the genome_Scope, we do not come to about the different types of repetitive element percentages in the genome, right??
I am sorry for the trouble and thanks a lot for the help.
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mschatz
commented on August 13, 2024
I would recommend you just use 21-mers for the analysis since that is the
value we have used for most of our testing. And as you said, GenomeScope
does not distinguish between different types of repetitive elements, other
than by their overall abundance in the data
The supplement for the GenomeScope paper has a detailed description of the
mathematics behind the analysis. Id recommend you start there
Good luck!
Mike
…On Mon, Oct 21, 2019 at 11:40 PM dlata123 ***@***.***> wrote:
Thanks for responding back, I wanted to confirm one more thing, I want to
use the Genome Scope approach in order to see the percentage of repetitive
elements in a genus of beetle, which has a genome size close to the human
being. In that scenario should I use a range of kmers size, and see by
using which size of kmer will give me minimum error rate, and choose that
particular kmer value to interpret the repetitive content of the genome.
???? This is just a thought because I read somewhere for a larger genome,
it good change kmer size.
Is there any place where I can read about the plots generated by the
genome_scope?? Lastly from the genome_Scope, we do not come to about the
different types of repetitive element percentages in the genome, right??
I am sorry for the trouble and thanks a lot for the help.
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Related Issues (20)
- 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
- Estimated genome size is half HOT 2
- Should a larger K value be chosen? HOT 1
- Is command line for ploidy different? HOT 4
- Please help me to understand output
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