SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
IDP - Isoform Detection and Prediction - new version 0.1.6 g3n3 Pacific Biosciences 2 06-02-2017 07:09 AM
Newbler sensitivity tuning for isoform detection? yvan.wenger 454 Pyrosequencing 2 12-06-2010 11:35 PM

Reply
 
Thread Tools
Old 09-27-2016, 01:45 AM   #1
dovah
Member
 
Location: Russia

Join Date: Jul 2014
Posts: 18
Default unique isoform detection using IsoSeq

Hi all,

I launched Iso-Seq on my RNA data (D. melanogaster). My aim is to see how many isoforms per gene are there in my sample. I am following the tutorial on github.

The Iso-Seq pipeline being completed, now I got the output in two folders: Cluster (for consensus isoforms) and Classify (for "real" sequenced isoforms).

I would need somebody to guide me in the interpretation of these folder content, since it is my first experience with Iso-Seq. I think that unique full-lenght (non-chimeric) isoforms in folder Classify are those reported in file: isoseq_flnc.fa and the unique consensus full-length in folder Cluster are reported in file: polished_high_qv_consensus_isoforms.fastq.
Is this correct?

How can I link the isoforms to the gene? Shall I blast it?

Many thanks for the help!
dovah is offline   Reply With Quote
Old 10-28-2016, 09:25 AM   #2
Magdoll
Member
 
Location: Bay Area

Join Date: Aug 2011
Posts: 30
Default

Hi,

Yes you are correct in your interpretation. Best way to proceed to visualizing isoforms:

-- take the HQ isoform output (polished_high_qv_consensus_isoforms.fastq) and align it to your genome. You can use a collapse script to remove some redundancy (there will be a little): https://github.com/PacificBioscience...nt-transcripts

-- to compare it with existing annotation, use matchAnnot (https://github.com/TomSkelly/MatchAnnot)

there's also a lightweight script that can parse matchAnnot results for you:
https://github.com/Magdoll/cDNA_Cupc...refaction-Wiki

I don't check seqanswers often enough, so apologies for the late response.

Please consider joining the public Iso-Seq google group. Response from there is usually much faster. You can certainly post on both Seqanswers and Google Group at the same time.

https://groups.google.com/forum/#!forum/smrt_isoseq
Magdoll is offline   Reply With Quote
Reply

Tags
isoform, pacbio, rna

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 04:23 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO