I just did a small test with one of the tools in this group with mm9 test data and the filter by species was fine. Perhaps something is not set up correctly? Or there is problem with a different tool (you didn't mention which in the set you were using, or I missed it!). Here is my test. If you can duplicate successfully, then maybe it will help you to determine where the problem is with your real data:
1 - Downloaded MAF data to my desktop from UCSC. Is small (1.7M), so I just used my browser and it was OK, but it is important to let it finish. http://hgdownload.cse.ucsc.edu/goldenPath/mm9/multiz30way/chrY.maf.gz
2 - Then again, since the file is smaller, just browser uploaded into Galaxy, setting the database as mm9. I could have also not set the database at upload and instead gone back and set the database using the "Edit Attributes" form (pencil icon) after upload completed.
3 - Obtained some sample interval data. Used "Get Data -> UCSC Main". From the mm9 database, RefSeq Genes track, limited to chrY, whole gene, BED format, sent to Galaxy. Double check metadata attributes. Since my data is from the UCSC Table browser, the defaults will be correct, but it is a good "best practice" to mention that it is usually worth a quick double check to confirm column assignments, datatype, and database assignments when using your own loaded/created data.
4 - tool: "Extract MAF blocks given a set of genomic intervals"
5 - set "Choose intervals:" to the dataset from step #4 and "MAF Source:" to "Alignments in Your History" then "Choose alignments:" as the dataset from step #2.
The list of species comes up under "Choose species:".
If you are still having problems after running this test, please feel free to send me a link to a shared history (use "Options -> Share or Publish", generate link, and email back directly to me, not to entire list). Please note which are the inputs if not obvious. Leave any error dataset in the history. In fact if there are any error datasets, you could use the green bug icon and submit the history that way and just mention in the but report comments that these are related questions.
Your question got a bit buried since it was sent as a reply to another thread. Next time, please send new questions as brand new questions, not as replies to prior questions with new subject lines. Helps greatly with tracking and such.
Hopefully this helps,
Jen Galaxy team
On 1/27/12 1:54 PM, Paralkar, Vikram wrote:
In the "Fetch Alignments" section, it's currently possible to get only human-projected alignments (from 46-way multiZ (hg19) MAFs). Any way you could add the ability to choose mouse-projected alignments? I tried to do this by downloading the multiz30way (mm9) MAFs from the UCSC browser to my history and using it as the "Alignment from your history", but then I can't choose specific species from the 30 species list.
Any way you could add the ability to choose mouse-projected MAFs, and then choose specific species from it, just the way you currently have for human-projection. Thanks.
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