"Realigner Target Creator" tool on usegalaxy.org Locally cached reference unavailable

Question: "Realigner Target Creator" tool on usegalaxy.org Locally cached reference unavailable

3.8 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

I have a bam file generated using a cached reference (not a user custom one). However if I sleet

'Choose the source for the reference list ' >Locally cached

The

'Using reference genome:' has no options.

Why is this are the cached references not suitable for this program?

THanks Guy

Tool name: Realigner Target Creator
Tool version: 0.0.4
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/realigner_target_creator/gatk_realigner_target_creator/0.0.4
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/realigner_target_creator

realigner-target-creator • 1.6k views

ADD COMMENT • link •

modified 3.3 years ago by pushpinderkaur2006 • 0 • written 3.8 years ago by Guy Reeves • 1.0k

3.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

On the public Main Galaxy instance at http://usegalaxy.org, there is only one built-in, or cashed, reference genome indexed for the GATK tools. This is the 1000 Genomes human reference genome "hg_g1k_v37". If you would like to use other reference genomes, use them as a Custom Reference genome with the tool.
http://wiki.galaxyproject.org/Support#Custom_reference_genome

Take care, Jen, Galaxy team

ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

HI Jen

I have gone through the documentation you sent again and have wrapped the .fasta (60 characters) file and used no spaces in the names when I make a ‘custom build’.

But I cant see how I will know if I have been successful. Should I be able to see the custom build name in the locally cached > Select reference genome: pop up menu? Will this occur on all or some tools.

Even after the Custom build has stopped ‘processing’ and correct number of chromosomes have been identified, I still cannot find the custom build anywhere.

Thanks

Guy

ADD REPLY • link written 3.8 years ago by Guy Reeves • 1.0k

Hello, Custom builds appear under User -> Custom builds and here you can note the progress (if it is still processing, wait for it to complete before moving forward with your analysis). Then, once ready, it can be found in the "reference genome/build" list on the Upload tool and also on the first Edit Attributes tab (click on the pencil icon per dataset to view this, and assign to a dataset as needed).

Some tools interpret the database assigned to input datasets. But, most have an option on the tool form to select a custom genome in fasta format from the history (this is just a dataset in the same active history, copy it around into other histories as needed - there is no real data duplication from a copy - it is just a clone dataset and will not impact your data quota). I am fairly certain that all tools on http://usegalaxy.org will function with one of these methods when using a custom genome/build.

Hopefully this helps, but let us know if you are still having some issues (along with the specific details). I can go into your account and examine all in detail if needed.

Thanks! Jen

ADD REPLY • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

3.3 years ago by

pushpinderkaur2006 • 0

United States

pushpinderkaur2006 • 0 wrote:

I am having a bam file generated using a cached reference (not a user custom one). I am facing the problem in

'Choose the source for the reference list ' >Locally cached

When I tried to use the reference genome 'Using reference genome:' has no options.

How can i fix this issue?

Thanks

Pushpinder

ADD COMMENT • link written 3.3 years ago by pushpinderkaur2006 • 0

Is this on usegalaxy.org?

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

Hi Bjoern,

Yes it is on usegalaxy.org

Thanks

Pushpinder

ADD REPLY • link written 3.3 years ago by pushpinderkaur2006 • 0

A member from the Galaxy core team will jump in and help you here.

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

Hello, The answer is mostly likely that the genome you are using has not been indexed for the tool you are trying to use. This means that the Custom genome method must be used instead. In the future, please post new questions as new threads, not inside of prior Q&A. If you feel that another post is relevant to your question, a link to the related post can always be included in the new question's post. Thanks, Jen

ADD REPLY • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

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