Trouble in extracting species on maf imported from UCSC
Hi, When I import a multiz46way maf alignement from UCSC, if is is a whole chromosome, then when I try to "Filter MAF blocks by Species" the list of species does not appear. If I import a small region, it works... Is it a question of size? Although it seems OK when I look at it, could it be a problem in the maf format that I could solve? Thank you, Aurelie
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 On 11/11/11 2:20 PM, 4urelie K wrote:
Hi,
When I import a multiz46way maf alignement from UCSC, if is is a whole chromosome, then when I try to "Filter MAF blocks by Species" the list of species does not appear. If I import a small region, it works... Is it a question of size? Although it seems OK when I look at it, could it be a problem in the maf format that I could solve?
Thank you, Aurelie
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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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 On 11/11/11 4:06 PM, Jennifer Jackson 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
On 11/11/11 2:20 PM, 4urelie K wrote:
Hi,
When I import a multiz46way maf alignement from UCSC, if is is a whole chromosome, then when I try to "Filter MAF blocks by Species" the list of species does not appear. If I import a small region, it works... Is it a question of size? Although it seems OK when I look at it, could it be a problem in the maf format that I could solve?
Thank you, Aurelie
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
participants (2)
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4urelie K -
Jennifer Jackson