SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
transdecoder vishwesh Bioinformatics 0 06-06-2014 01:39 AM
snpEff error sinnamone Bioinformatics 3 05-14-2014 11:05 PM
snpeff mmmm Bioinformatics 3 04-04-2014 06:54 AM
snpeff warnings mmmm Bioinformatics 2 01-23-2014 04:57 AM
snpEff annotation omerfaruk Bioinformatics 1 01-06-2014 12:25 AM

Reply
 
Thread Tools
Old 01-06-2015, 12:38 AM   #1
vinaydu
Member
 
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
Reply

Tags
snpeff transdecoder

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:59 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO