SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Weird pileups mjlarsen Illumina/Solexa 0 05-14-2019 05:58 AM
Weird DE-results ErikFas Bioinformatics 9 02-18-2015 10:08 PM
Weird quality issue MikeT Ion Torrent 4 06-16-2014 09:09 AM
weird fpkm value bioliyezhang Bioinformatics 2 10-11-2012 01:04 PM

Reply
 
Thread Tools
Old 05-27-2020, 07:02 PM   #1
sannazza
Junior Member
 
Location: Argentina

Join Date: May 2019
Posts: 3
Question weird annotation, please help!

Hi!
I've sequenced a bacterial genome using PacBio, de novo assembled it using three different assemblers (canu, flye and unicycler). They all worked more or less ok, and the assembled genome is around the expected size for the genus (around 7Gb). But when I try to annotate it, no matter if I use any of the three assemblies or two different programs (Prokka or RAST) I always get way too many more genes than other related species (9937 vs ca. 6500).
Any ideas of what could be happening? I'm really stuck here and can't figure out what is going on, so any help will be much appreciated!
Cheers
Ana
sannazza is offline   Reply With Quote
Old 05-28-2020, 06:53 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076
Default

Have you tried to use an assembly reconciliation tool? There may be a newer reference than this one of such tools.
GenoMax is offline   Reply With Quote
Reply

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 07:34 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO