spliceR: problems in detecting NMD sensitivity from RNA-seq data

[znasim09]

Hello everyone,

I want to detect the NMD sensitivity from RNA-seq data of my Arabidopsis mutants. I read that spliceR can be used for this. However, spliceR requires CDs from UCSC, that does not support Arabidopsis.

So, my questions are:
1) How can I use this command for Arabidopsis:
annotatePTC(transcriptData, cds, genomeObject, PTCDistance=50)

as the cds here comes from UCSC (ucscCDS <- getCDS(selectedGenome="hg19", repoName="UCSC") and Arabidopsis genome is not supported by UCSC.

2) Are there any other tools that can be used to detect PTCs/NMD sensitivity??