Thank you Jen. You mentioned it may be a formatting problem and you were
able to successfully convert the coordinates to mm8. I tried that several
times yesterday and they kept coming up in the unmapped file saying the
region was deleted from the newer build. I opened the tab deliminated text
file I created in Excel in Notepad++ and just resaved it without changing
anything. When I uploaded the new file to galaxy and and lifted over to
mm8 it worked fine. It still wouldn't pull out genomic sequences from mm7,
but it will from the new file converted to mm8. Thank you for your help -
it is very much appreciated!
On Wed, Oct 30, 2013 at 11:45 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:
> Hello Jill,
> This is strange. I just pasted the region you noted below into Galaxy (in
> the 'Get Data -> Upload File' tool), assigned it to mm7, and lifted to mm8
> without any issues. I also checked the data behind the tool - all appears
> to be fine.
> result in mm8 coordinates
> Are you certain there is not a format problem with the data? This seems to
> be the only explanation for the problem. But after one more check, you can
> submit a bug report and note that this is the problem. Be sure to leave the
> input and all error outputs undeleted when you report the problem or we
> won't be able to offer the best feedback.
> It is true that UCSC only produced a liftOver file that went from
> mm7->mm6/8, then you can go from mm8->mm7/9/10. This is just the data
> available. When lifting from data this old - be aware that a genome can
> change quite a bit in some regions in new 3 revisions. Still, lifting this
> way is certainly something you can try. If a much older genome is not in
> Galaxy, just do the lift at UCSC (the liftOver tool is under the top blue
> banner "Tools").
> Hopefully the problem can be sorted out but if not we can take a look,
> Galaxy team
> On 10/30/13 3:04 PM, Kreiling, Jill wrote:
> Hello, I have a set of coordinates for mm7 that I have been using try
> to extract the genomic sequences. However it doesn't recognize the
> chromosome name column. The are currently listed as chr1, chr2, ....chrX.
> This is the error I get each time I try to extract sequences:
> Chromosome by name 'chr1' was not found for build 'mm7'. Skipped 1181
> invalid lines, 1st is #1, "chr1 4558068 4561910 region_0 0 +"
> However if I change the build to mm10 it works fine - but the
> coordinates are not the same between builds. Also, mm7 can't be lifted
> over to mm9 or mm10.
> Does anyone know the proper format for chromosome name in mm7:
> The Galaxy User list should be used for the discussion of
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> Jennifer Hillman-Jacksonhttp://galaxyproject.org
Jill Kreiling, Ph.D.
Assistant Professor, Research
Department of Molecular Biology, Cell Biology and Biochemistry
Providence, RI 02903
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:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
To search Galaxy mailing lists use the unified search at: