Question: where is locally cached sequence/ alignment data in Galaxy?
0
gravatar for biofilia
15 months ago by
biofilia0
biofilia0 wrote:

Hi, Does anyone know how to access the locally cached alignment files (MAF)? On the website: Under "Fetch Alignments/Sequences" > "Extract MAF blocks", you get to a screen with a pull-down menu labeled "MAF source". Here, there is an option "Locally cached alignments", however clicking on it does nothing. Am I missing something? Thanks, Merwin

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ADD COMMENTlink modified 15 months ago • written 15 months ago by biofilia0
1
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The database metadata assignment for the input interval file needs to be assigned. Currently at Galaxy Main (http://usegalaxy.org), MAF indexes are available for the genome databases hg19 and dm3.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 15 months ago • written 15 months ago by Jennifer Hillman Jackson25k
0
gravatar for biofilia
15 months ago by
biofilia0
biofilia0 wrote:

Thanks, Jen.

I added a metadata line to my interval data file, but under "Choose MAF source" it still says "No options available." This is the first two lines of my interval file:

track name=pleioRegions db=hg19
chr3 3400000 4500000 1 0.3 +

Any idea of what I'm doing wrong?

Thank you, Merwin

ADD COMMENTlink modified 15 months ago • written 15 months ago by biofilia0
1

Hello,

The track line is not needed and may cause other problems with this tool. Instead, assign the hg19 database to the dataset itself. Do this by clicking on the pencil icon (top right corner of a dataset's box in the history) and changing the database assignment on the Edit Attributes forms that come up in the middle pane and save.

Best, Jen

ADD REPLYlink written 15 months ago by Jennifer Hillman Jackson25k
0
gravatar for biofilia
15 months ago by
biofilia0
biofilia0 wrote:

Hi Jen,

That worked perfectly, Thanks!

Merwin

ADD COMMENTlink modified 15 months ago • written 15 months ago by biofilia0
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