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
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