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Old 09-10-2015, 12:03 AM   #1
huan
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Question how to extract alternative splicing information from Iso-seq nonredundant sequence?

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. So now I have the isoform consensus result. But I don't know how to extract the detail alternative information (including alternative type, alternative start site, alternative end site). I don't know any software or script can do this?


What is the best approach?


Thanks for any comments in advance.
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Old 09-13-2015, 10:01 PM   #2
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Is there any software or script can do the analysis in the poster 'Rapid Full-Length Iso-Seq cDNA sequencing of Rice mRNA to Facilitate Annotation and Identify Splice-Site Variation'?[Poster_RapidFullLength_IsoSeqcDNASequencing_RicemRNA.pdf]
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Old 09-16-2015, 06:55 AM   #3
rlleras
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Hello Huan,

So in order to identify the things you are looking for, the easiest path forward is to align your transcripts to a reference genome with a splice site aware aligner like GMAP then identify PacBio transcripts that share anchor points.

There are tools like Tom Skelly's MatchAnnot (https://github.com/TomSkelly/MatchAnnot/wiki) that will allow you to compare your aligned PacBio transcripts to a previous annotation file that you might have access to. This will allow you to sort previously identified transcripts from unknown transcripts (ie alternative start sites, splicing, etc).

-Roberto
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Old 09-17-2015, 08:33 PM   #4
huan
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Quote:
Originally Posted by rlleras View Post
Hello Huan,

So in order to identify the things you are looking for, the easiest path forward is to align your transcripts to a reference genome with a splice site aware aligner like GMAP then identify PacBio transcripts that share anchor points.

There are tools like Tom Skelly's MatchAnnot (https://github.com/TomSkelly/MatchAnnot/wiki) that will allow you to compare your aligned PacBio transcripts to a previous annotation file that you might have access to. This will allow you to sort previously identified transcripts from unknown transcripts (ie alternative start sites, splicing, etc).

-Roberto
Thanks a lot rlleras! It seems help a lot!
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