how to extract alternative splicing information from Iso-seq nonredundant sequence?

[huan]

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.

[huan]

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]

[rlleras]

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

[huan]

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!