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
chr14552557 4556399 region_00 +
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,
Jen
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:
Thanks,
Jill
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Jennifer Hillman-Jackson
http://galaxyproject.org
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