SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Genome assembly using Pacbio sequel data yjpark1091 Pacific Biosciences 5 11-29-2017 08:32 AM
New PacBio system: Sequel SNPsaurus Pacific Biosciences 62 09-28-2017 04:33 AM
Pacbio sequel for single cell human WGS? WhatsOEver Pacific Biosciences 5 06-27-2017 11:02 AM
variant calling from pacBio Sequel data splaisan Bioinformatics 0 03-25-2017 06:20 AM
PacBio Sequel demultiplexing Ali May Pacific Biosciences 4 12-06-2016 09:43 PM

Reply
 
Thread Tools
Old 04-22-2018, 10:58 PM   #1
yjpark1091
Junior Member
 
Location: Kyungpook Nat'l Univ. in South Korea

Join Date: May 2017
Posts: 4
Default Ploidy estimation or decision using pacbio sequel data

Hi all.

After finish assemble fungus genome from pacbio sequel using SMRT link or Falcon assembler, the genome size is twice as much as I expected.

So, I want to get your advice or opinion for estimation or decision of ploidy of Fungal genome from Pacbio Sequel platform.

Actually, the fungus genome was extracted using mycelia and spore.
(I think this is a mistake that I made...)

In my search, most of program for ploidy estimation are focus on short read such as illuminal Miseq and Hiseq.

If there are good opinions or comments, and ideas please tell me about that.

Best regards,
YJ

Last edited by yjpark1091; 04-22-2018 at 11:01 PM.
yjpark1091 is offline   Reply With Quote
Old 04-29-2018, 10:46 AM   #2
kramergj
Junior Member
 
Location: Toronto

Join Date: Nov 2015
Posts: 3
Default

Hi there,
I am interested in hearing how you ended up handling this. I suppose I do not have a definitive answer for your question, but any chance that you have a reference to compare to? If you take a closer look at your assembly, it would be interesting to see if you have "duplicated" chromosomes (provided your assembly allows you to make an assessment about chromosomes) as that I think could be indicative of a diploid (or polyploid, etc.) genome.
Glenna
kramergj is offline   Reply With Quote
Reply

Tags
diploid, fungus genome, haploid, pacbio, ploidy

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:15 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO