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Old 09-17-2015, 09:10 PM   #1
huan
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Question Is There Any Tools/Methods For PacBio IsoSeq SNP/Fusion Genes Analysis?

Hi, there!
I have used pacbio SMRT Iso-seq module to analyze my cDNA sequencing data, including Getting full length reads, Isoform level clustering (ICE and Quiver), Removing redundant transcripts. And I have got the isoform cluster result. Then I want to do the SNP , gene family or fusion genes analysis, but most of the publications show that this must be accompanied with the short-read sequencing data(eg. HiSeq data). So is there any analysis method can do with only pacbio Iso-seq data?


Thanks a lot for any apply
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Old 09-18-2015, 12:28 AM   #2
Bukowski
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There's some guidance on the Iso-Seq pages:

https://github.com/PacificBioscience...d-fusion-genes

I believe it refers to this paper:

http://nar.oxfordjournals.org/conten...ar.gkv562.full

And in particular this package:

http://www.healthcare.uiowa.edu/labs/au/IDP-fusion/
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Old 09-22-2015, 05:54 PM   #3
huan
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Thank you very much for your help,Bukowski! Your answer is very helpfull
I have already used the IDP-fusion pipeline for my dataset. It proves work great!
By the way, Is there any pipline for identifying-gene -amily analysis without the use of Hiseq data?
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Originally Posted by Bukowski View Post
There's some guidance on the Iso-Seq pages:

https://github.com/PacificBioscience...d-fusion-genes

I believe it refers to this paper:

http://nar.oxfordjournals.org/conten...ar.gkv562.full

And in particular this package:

http://www.healthcare.uiowa.edu/labs/au/IDP-fusion/
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Old 09-28-2015, 11:11 AM   #4
Magdoll
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What do you mean by gene family analysis?

If you want to know which isoforms may come from the same gene family, there are a few possibilities.

--- map it back to the ref genome. this gets you per-locus information. won't tell you which ones are orthologs, though.

--- BLAST against known genes?

--- do ORF prediction and cluster by the predicted ORFs. For the ORF prediction you can use ANGEL (https://github.com/PacificBiosciences/ANGEL) but I personally don't have much experience with clustering proteins. One possibility is to then take the predicted ORF sequences and do a PFAM scan to identify domains.
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