Question: how can I translate my GenomeScope results? Is it make sense?
0
gravatar for dongseokkim6662
13 months ago by
dongseokkim66620 wrote:

When I tried to use default option of jellfyfish and GenomeScope, it could not make the result. It said that profile cannot converge... So, I tried to adjust the kmer value and Max kmer coverage, such as 17 kmer, Max kmer coverage = 1,000,000. And then the results was emerged. But, I think this results is weird. Is it possible to make negative value of unique length?

You can check my results in below link.

http://genomescope.org/analysis.php?code=0b75l7MdAaX4mz64TSKa

sequencing kmer assembly genome • 429 views
ADD COMMENTlink written 13 months ago by dongseokkim66620

Can you tell us what kind of sequencing this is? What is the expected genome size? How much sequence you have?

ADD REPLYlink written 13 months ago by genomax85k

I did Illumina Novaseq6000. The expected genome size is about 20~30Mb because the genome size of the other species which is same genus is about 25Mb. And I sequenced the species about 26Gb.

ADD REPLYlink written 13 months ago by dongseokkim66620

so you sequenced it ~1040x coverage ?

ADD REPLYlink written 13 months ago by lieven.sterck8.0k

yes, we usually sequenced samples about 20Gb (illumina)

ADD REPLYlink written 13 months ago by dongseokkim66620

that's a serious overkill for such small genomes and will likely rather hinder the assembly process than improve it. Downsampling might be an advisable strategy here.

What you do you mean by 'usually' ? I would assume you estimate your seq-depth by the genome specs you want to sequence, no?

ADD REPLYlink written 13 months ago by lieven.sterck8.0k

yes, you can play (tweak) the params a little, and sometimes you will indeed have to even. However I'm afraid the parameters you mention here are not making much sense. Often you might also simply not have enough data to do the maths on (eg. coverage too low).

anyway, from the output you get you could have noticed your parameters are not making much sense, as you get a negative! fraction of uniq sequences in your dataset apparently ;)

ADD REPLYlink written 13 months ago by lieven.sterck8.0k

Thanks for replying my question. :)

ADD REPLYlink written 13 months ago by dongseokkim66620
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1802 users visited in the last hour