View Single Post
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