Bowtie for Illumina using reference genome of pisifera oil palm tree

4.6 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

A Custom Reference Genome can be used with most tools and doesn't really even need to be genomic sequence. It can be any fasta sequence file. If highly fragmented, you may run into memory issues, but you won't know until you try. And if that does occur, moving to a cloud Galaxy can often help (with increased dedicated memory).

Here is how to get started with a Custom Reference Genome (few quick steps): https://wiki.galaxyproject.org/Support#Custom_reference_genome

Look for the "Cloud" link in the side bar of the wiki, should you need to go in that direction.

Best, Jen, Galaxy team

ADD COMMENT • link written 4.6 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you Jen,

I want to use Galaxy as a platform for collaboration between several experimental laboratories, but our data is not yet available for public use. Do you encrypt data? Is data protected from public use?

Is there a way to run BioBase Transfac Match Professional Version on Galaxy to find transcription factors binding sites?

We have several private tools like Match from BioBase that are not yet published. Is there a way to imbed them into your platform and have them for our own private use?

Can I add my own gene annotations for my own reference genome (or even scaffolds) and visualize data using your platform?

May be you have all these in relatively inexpensive version of Galaxy for academia?

Thank you. Petr.

From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: Wednesday, May 07, 2014 4:51 PM To: Ponomarenko, Petr Subject: [galaxy-biostar] A: Bowtie for Illumina using reference genome of pisifera oil palm tree

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: Bowtie for Illumina using reference genome of pisifera oil palm tree<http: biostar.usegalaxy.org="" p="" 7497="" #7503="">:

Hello,

Here is how to get started with a Custom Reference Genome (few quick steps): https://wiki.galaxyproject.org/Support#Custom_reference_genome

Look for the "Cloud" link in the side bar of the wiki, should you need to go in that direction.

Best, Jen, Galaxy team

ADD REPLY • link written 4.6 years ago by pponomarenko • 0

Hello,

For sensitive data and to incorporate your own tools, a cloud Galaxy is recommended. Here is how to get started:

http://usegalaxy.org/cloud

And this is the information for how to wrap tools:

https://wiki.galaxyproject.org/Admin/Tools

When it comes time to publish your tools, please consider the Tool Shed:

http://usegalaxy.org/toolshed

https://wiki.galaxyproject.org/ToolShed

Good luck! Jen, Galaxy team

ADD REPLY • link modified 4.6 years ago • written 4.6 years ago by Jennifer Hillman Jackson ♦ 25k

Similar posts • Search »