SEQanswers

Go Back   SEQanswers > Applications Forums > De novo discovery



Similar Threads
Thread Thread Starter Forum Replies Last Post
Trinity genome guided error sandesh Bioinformatics 0 04-22-2015 12:56 PM
Genome guided Trinity ysnapus Bioinformatics 0 09-17-2014 11:13 AM
Compare de-novo transcriptome assembly to genome reference guided assembly IdoBar Bioinformatics 1 04-04-2014 12:28 AM
Map transcripts from de novo assemblier such as trinity back to the genome ? sptmbr Bioinformatics 5 02-29-2012 09:47 AM

Reply
 
Thread Tools
Old 10-08-2015, 03:52 AM   #1
Mocca
Junior Member
 
Location: Oslo

Join Date: Mar 2012
Posts: 9
Default Genome guided vs de novo - Trinity

Hi everyone,

For a while now I have been working on my de novo Trinity assembly (fish species). Using my de novo transcriptome I have been able to do some interesting differential expression analyses. Then the genome-guided option of Trinity was launched and I tried it using the second version of our draft genome. I didn't use the first genome version as some of my genes of interest were poorly (wrong) assembled and also, on occasion, partially within gaps. Now this is mostly corrected and I hoped that doing the genome guided Trinity would reduce the number of transcripts. I went from 320520 'genes' and N50 1235 to 342099 'genes' and N50 1716.

So better N50 but more transcripts... Also, if I do abundance estimation a FPKM cutoff of 2 for the first gives ~30 000 'genes' and the second ~119 000 'genes'.

Based on stats only - which would you chose to use for DE analysis? Considering redoing Trinotate and all DE analyses with the genome guided version.

Any thoughts are most welcome
Mocca is offline   Reply With Quote
Old 10-09-2015, 05:24 AM   #2
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 817
Default

Genome guided should be better with a good reference genome. The main disadvantage is that transcripts will only be generated if they are supported by the genome, so if the reference genome assembly is incomplete then there might be a few missed transcripts.
gringer is offline   Reply With Quote
Old 10-09-2015, 09:54 AM   #3
Mocca
Junior Member
 
Location: Oslo

Join Date: Mar 2012
Posts: 9
Default

Discussing the quality/"completeness" of the genome with my collaborators migth be the next step then. I also got a bit hung up on the abundance estimation analysis with the FPKM 2 cutoff where the number of transcripts suddenly fit the number of predicted genes for my species using the de novo assembly but not the genome guided assembly. Could just be coincidences though.

If I had a complete list of "genes of interest" I could check if they were assembled properly in the genome/transcriptome, but I'm also searching for alternative responses to treatment so...

Contemplating a bit more :-)
Mocca is offline   Reply With Quote
Reply

Tags
de novo, genome guided, rnaseq, trinity

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 07:24 PM.


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