Hi Everyone:
I am trying to go through analysis of alternative splicing from RNA-seq. So far I have got the coordinates of some intron, and I want to analyzed the feature of these intron: GC contents, whether and where it will generate premature stop codon, strength of 5' or 3' splice site.
Is there good package to use for these analysis?
Thanks
Cai
If you want to analyse the consequence of alternative splicing you need transcript level quantification of events (since the consequence of an intron retention depends on all of the connected up and down-stream exons). You can read more about different approaches to analysis of splicing here. Also if you want transcript level quantifications you can read more about such considerations here. My R package IsoformSwitchAnalyzeR will enable you to find such cases quite easily - both on a genome wide level and of individual genes - you can find examples of the analysis produced by the package here.
In terms of analysing biological sequences the Bioconductor package Biostrings is a very nice set of tools for doing so. You can find a nice example of how people use it to calculate GC content of CpG islands here.
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Thank you very much for your advice. I am going to give it a try
Hello:
I read about the manual, it is comprehensive but intimidating for me. I want to give it a try on the data I have. So far I have run RSEM to do the quantification of the isoform. I have a file called "rsem.isoforms.results", but I have no idea of how to use it. Do you have a step by step manual. The manual from the link import data from the package which I don't know how to use in my case. Thanks
IsoformSwitchAnalyzeR can work directly from the "rsem.isoforms.results". I suggest you take a look at the quick start part of the vignette which should describe exactly what you need including code you can use.
OK. I will read it again to make it through.