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Old 01-06-2015, 12:38 AM   #1
Location: Delhi

Join Date: Dec 2010
Posts: 17
Default snpeff with transdecoder

Dear all,

I need your help regarding an analysis which uses your tool snpeff. I am working with a system which do not have reference genome. I have RNA-seq reads for two species which I assembled de-novo using Trinity. I found variant between them using freebayes. To use snpeff, I used unigenes (called using cd-hit) of one species as reference which is annotated using transdecoder. I have used transdecoder generated gff file and the fasta file to make bins for snpeff.

Odd enough, I found introns, intergenic regions downstream, upstream which I think should be not there in EFF= field. Am I missing something?

In a nutshell could snpeff be used for de novo transcriptome assembly?

Prompt response would be highly appreciated on my part.

Thanks in advance
vinaydu is offline   Reply With Quote

snpeff transdecoder

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