Question: UCSC Comparative Genomics MAF and Galaxy
1
gravatar for amandine.bery
5 months ago by
amandine.bery10 wrote:

I am looking for conserved non coding elements (CNEs). I was used to use Table browser in UCSC and Comparative genomics from Custom tracks made of BED file. I was choosing to send the output file (MAF file) in Galaxy. However it is not working anymore. Galaxy provide a MAF file but is not able to identify the MAF blocks (? Blocks). Please, can you help?

Amandine P.S.: How can I attached the BED file?

conservation ucsc galaxy maf • 196 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by amandine.bery10
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

I suspect there is a format, content, or metadata problem interfering with the query. A tool issue is a potential, but checking the inputs first is where to start. If there is a tool problem, we want to learn about it and fix it.

I cannot find your account at Galaxy Main https://usegalaxy.org to troubleshoot whether it is the datatype assignments, true tool error, or input content/corruption (possibly an incomplete data transfer from UCSC - the export file line limit is around 100k from the Table browser - for anyone, not just Galaxy). For most MAF data, it is so large that it needs to be loaded from the UCSC downloads server, not the Table Browser. How-to: locate the files at UCSC (genome name > conservation tracks), download locally using their instructions, then FTP the data to Galaxy.

Choices:

  1. You can try to troubleshoot yourself with this FAQ help: https://galaxyproject.org/support/#troubleshooting
  2. Or if your account is at Galaxy Main, send us an email at galaxy-bugs@lists.galaxyproject.org from your registered account email asking for help (private list) and that will help us to locate it. Including a share link to the history in the email would be helpful but is not necessary, you could also note the history/dataset names/numbers in the email text (but do not delete these problematic datasets or histories if you want feedback). FAQ: https://galaxyproject.org/issues/#usage-problem-reporting
  3. Or, if you are not working at Galaxy Main right now, you could try to reproduce the problem there. If you can, please ask for help as in #2. If you cannot reproduce the problem, then you will need to contact the admins of the server you are working on. If you are the admin, make sure you are running the latest version of Galaxy (these tools are part of the core distribution) after first checking the inputs.

Please let us know how this works out! The tools are known to work when given the proper inputs but a new tool problem is always a possibility. We can help to figure out which and resolve it.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k

I do not want to download all MAF from UCSC download. I want only the MAF file from the input BED file that includes my selected sequences.

ADD REPLYlink written 5 months ago by amandine.bery10
0
gravatar for amandine.bery
5 months ago by
amandine.bery10 wrote:

I do not want to download all MAF from UCSC download. I want only the MAF file from the input BED file that includes my selected sequences

ADD COMMENTlink written 5 months ago by amandine.bery10

Subsetting MAF data is what the tools in the group Fetch Alignments/Sequences do. But you'll need an intact MAF dataset as an input. This is usually the entire genome or a complete targetted chromosome (or chromosomes). Once the data is reduced, the original full MAF can be permanently deleted to recover disc space in your account.

Also - I see your email to the bugs mailing list. I am reviewing and will reply there with more details for troubleshooting the problems.

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
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