Question: Need help with "Tophat2" tool
gravatar for martine.collart
4.4 years ago by
United States
martine.collart0 wrote:

Is there no yeast genome as a reference for using Tophat2 in Galaxy? I only found sc2 and sc3 it for using Bowtie. Martine


Tool name: Tophat2
Tool version: 0.6
Tool ID:
ToolShed URL:


ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by martine.collart0
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Correct, the sacCer* genomes sourced from UCSC are still pending release of bt2 indexes (permit use with the tools Bowtie2 & Tophat2).

I clarified that his was in fact on "next batch processing" list of genomes and added it specifically to the public Trello ticket where requests are included. You can follow the genome there (the ticket may branch, but this will be noted with links):

The final list of all genomes processed will be published once the processing cycle is near completion. However I can let you and others know some of the general goals I have for this next cycle:

  1. Time frame: July-Aug/Sept-Oct 2014
  2. Number of "snapshots": likely at least two, perhaps more
  3. Data will release to the public Main Galaxy instance ( plus the rsync server hosted by use for use by local/cloud Galaxy instances or line-command/external processes that interact with Galaxy (
  4. Content will focus on the remaining UCSC mammals and vertebrates not currently included. (Completely new, plus updates/additions for existing, to fully index each).
  5. Certain invertebrates and plant/bacteria/fungi will be included

Until that time, and no matter where you are working, (sc2 and sc3 appear to be variations on these genome names, so you may at another public Galaxy site?) - you will also certainly be able to use the "Custom Reference Genome" option unless this functionality has been disabled. The size of the yeast genomes is well within the range that executes successfully even on conservative instances. You can obtain the fasta version of the genome from our rsync or from UCSC directly. Link to help:

Hopefully this helps you to move forward now via the Custom option, and provides some information about our plans this summer for genome processing for the curious! I'll be the one primarily working on this, but everyone on our team works in collaboration - genome questions/requests can be sent into Galaxy Biostar (new question == new post please!) and we'll clarify.

Take care, Jen, Galaxy team

ADD COMMENTlink written 4.4 years ago by Jennifer Hillman Jackson25k
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