I have transcriptome assemblies from two closely related species. One of them is well characterized (e.g. start and stop of coding region), but the other is more of a de novo transcriptome assembly. The expected sequence divergence should be less than 1%.
I want to first identify polymorphisms and then characterize them (synonymous substitution vs. non synonymous substitution, Indel cause reading from shift etc.). What are the best tools to get this information?
I have used Varscan to identify polymorphisms but it doesn't specificy whether mutations are synonymous or not. I am also interested in using a sequence alignment based method to cross verify Varscan results.
I think snpEff (http://snpeff.sourceforge.net/) could help you.. you need to create the files needed as input to create your own organism DB (take a look at this page http://snpeff.sourceforge.net/SnpEff_manual.html#databases)... if you have proper annotation files then its possible... the author is actively replying and help fixing issues.. you can write to him ([email protected]) about your issue...
these articles might be of some interest to U.
De novo Transcriptome Assembly and SNP Discovery in the Wing Polymorphic Salt Marsh Beetle P.....
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0042605
De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris ......
http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2011.03079.x/abstract
I suggest to read this article : http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003457
You can use VarScan. This software is extensively used and documented. More information in:
http://varscan.sourceforge.net/
http://www.ncbi.nlm.nih.gov/pubmed/22300766
Regards,
Leandro
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