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How to download the data
08-Nov-2013, 10:19 AM
Post: #1
How to download the data
Hi All,

We had the following query from a user and as it may be of interest to others, I'm posting it here:

"Is it possible to download all the data for large scale use .. (e.g. the densities of all the genes in all the organisms that you have)?"

It is possible to download the alignments (in BED format) for each of the tracks for the different organisms.

Click on the "Tables" tab in the top line of the browser.
Select the genome of interest.
Under group, select the type of data of interest, eg ribosome profiles of elongating ribosomes,
Select the track (cell line/Study).
Under table, select the condition.
Select "genome" for the region.
Click on "create" beside the Filter option and select 10,000,000. This is the current upper limit, but it should be sufficient for most tracks.
Select "data points" for the output format and "gzip compressed" for file type, and click "get output".
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16-Feb-2014, 02:41 PM
Post: #2
RE: How to download the data
Hi, audrey!

GWIPS is a powerful website for scientist, as it is a lot of work to mapped all this datasets. I wonder if it is possible to download the file produced by RUM as 10,000,000 is still insufficient, because I want to know coverage of every position.

Thank you very much!
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17-Feb-2014, 12:48 PM
Post: #3
RE: How to download the data
Hi,

I have added "1,000,000,000" to the filter option. This should be sufficiently large so that all coordinates that have coverage can be downloaded (in BED format) for the tracks in GWIPS-viz.

Can you let us know if you can now download the track(s) of interest to you?

Thanks again for your support,
Audrey
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18-Feb-2014, 12:52 PM
Post: #4
RE: How to download the data
Hi, Audrey.

There are 36 genes that I want to know whether they are covered by ribosome reads, open all Ribosome-profile tracks would be a choice. But my gene list would be expanded to more than one hundred, so raw file may be need in my script. Anyway, I can view each gene in GWIPS-browser at the moment.

Thank you for your reply!
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