Question: Rnaseq Clostridium Butyricum
gravatar for Benoit HENNUY
7.1 years ago by
Benoit HENNUY20 wrote:
Hi, I would like to use Galaxy with RNAseq data generated from "Clostridium butyricum" species. Please, could you include this genome in your list ? Thank you in advance Best regards Benoit HENNUY
galaxy • 761 views
ADD COMMENTlink modified 7.1 years ago by Jennifer Hillman Jackson25k • written 7.1 years ago by Benoit HENNUY20
gravatar for Jennifer Hillman Jackson
7.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello, The quickest way to use this genome is to load it into your history in fasta format. Use FTP, as described here: Then, use the "NGS: RNA Analysis" tool set's first step TopHat with the option "Will you select a reference genome from your history or use a built-in index?: Use one from the history". Most of Galaxy's mapping tools have this option, although it may be named slightly differently on the tool forms. A double check that your uploaded reference genome has the same exact identifiers present in any reference annotation GTF file you plan to use in later steps is a good idea. This will ensure that the TopHat mapping results will be interpreted correctly by the Cuff* tools. Even minor differences in chromosome/scaffold names will cause problems and it is easier to align the naming conventions up-front. Tutorial and FAQ: Best wishes for your project, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 7.1 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour