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Question: How to study just one stretch of a certain chromosome for transcribed RNAs.
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gravatar for english.srver
3.1 years ago by
english.srver • 0
Australia
english.srver • 0 wrote:

Hi all,

I am new to Galaxy. How can I study just one stretch of a certain chromosome for transcribed RNAs? I need this because of my low internet speed. Thank you in advance.
rna-seq one strech of a chromosome • 683 views
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modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by english.srver • 0
1
gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Are you trying to visualize data or run an analysis? Neither should be impacted by your internet connection speed.

Even large data can be uploaded through FTP on slower connections (use Filezilla, and if/when a time-out occurs, just resume the transfer).

If using a genome browser (Trackster, UCSC, IGV, there are many options), regions can be specified for visualization.

For most analysis, it is best to map across the entire genome first, then focus on a smaller region (a particular chromosome or part of one). How to filter for just a specific region depends on the analysis/tools/data formats, but Galaxy has many tools to subset/filter data for the most common types of formats. Try a tool search by the datatype to find these.

Hopefully this helps but if not please describe what you want to do in more detail. Thanks, Jen, Galaxy team

 
ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you for your response. I want to run an analysis from available data on public databases. My internet speed is 256 Kb and upload speed is ~ 8 KBytes/sec.

ADD REPLY • link written 3.1 years ago by english.server • 0

If you are able to load the data directly from one public server (data source) to another (a Galaxy server), using a "Get Data" tool or a URL with the Upload tool, then none of the data transfer work will be dependent on your internet connection speed. Often there is no need to download data locally to your own computer then upload it to Galaxy. Move the data directly between servers.

Data source server: look under "Get Data" for common ones but most data publically available via URL can be loaded (the exception would be a .tar.gz compressed archive, which needs to be uncompressed locally before loading the contents)

Public Galaxy server: http://usegalaxy.org or review the list here https://wiki.galaxyproject.org/PublicGalaxyServers

ADD REPLY • link modified 3.1 years ago • written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you indeed very much.

ADD REPLY • link written 3.1 years ago by english.server • 0
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