Trouble In Extracting Species On Maf Imported From Ucsc

7.1 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Aurelie, Would you have time to share a history link containing the two types of datasets for me? Use "Options -> Share or Publish", generate the link, then email it back to me directly. Please note the dataset(s) with the issue if not obvious (or make a note about it in the "info" field of the dataset). I will watch for your feedback, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Aurelie, The dataset from the UCSC Table browser did not transfer completely, which lead to the other errors. There is a limit to the number of rows of data that can be extracted, to Galaxy or any other type of download. It is around ~100k, but it depends on the data type. The UCSC group would have the details. To access human hg19 MAF data in Galaxy, use these tools, then proceed with the rest of your analysis: - Extract Pairwise MAF blocks given a set of genomic intervals - Extract MAF blocks given a set of genomic intervals Thanks for sending the link and hopefully this option will work for your project, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD REPLY • link written 7.0 years ago by Jennifer Hillman Jackson ♦ 25k

What if the task is to do this with mm10, for which you do not have MAF data in Galaxy (and importing it via table browser or file download/upload does not work)???

ADD REPLY • link written 4.0 years ago by dvanic • 0

Hello,

There are two choices for loading large data files from other public sources:

1. download the files directly from UCSC, then load those into Galaxy via FTP

2. paste the URL of the data file directly into the Upload tool (at the top of the tool panel) or into the Get Data -> Upload file tool.

The first will show progress. And both accept most compressed file formats. Note that this will only work with public datasets (UCSC's are public).

This details for how to use the second tool are in our wiki here.
http://wiki.galaxyproject.org/Support#Loading_data

The first tool has documentation that we'll be linking in, but it is fairly intuitive to use, especially after reviewing how the second one works

Thanks, Jen, Galaxy team

ADD REPLY • link written 4.0 years ago by Jennifer Hillman Jackson ♦ 25k

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