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I was recently asked how to save the sequence of a "random" location in JBrowse 2 (that is, not the sequence of feature like a gene). While the "save track data" option available on the git branch of the same name sort of works, it has problems in this instance. Given this location:
and selecting "save track data" from the track ... menu, I get a dialog to save. GFF and BED don't really make sense in this context, so select GenBank (fasta would be a good option here too). The result looks like this:
Note the fractional coordinates: V:13707382.014586711..13707915.014586711. In some cases while look at this bug, I found that it also got the starting base wrong if the fraction was a little less than the starting coordinate (like it's doing a int of the coordinate, which is not terribly unreasonable, but would be wrong in this case).
Version:
JBrowse 2.6.3 (haven't had a chance to test with newer version yet) in Firefox
Additional context
The text was updated successfully, but these errors were encountered:
Describe the bug
I was recently asked how to save the sequence of a "random" location in JBrowse 2 (that is, not the sequence of feature like a gene). While the "save track data" option available on the git branch of the same name sort of works, it has problems in this instance. Given this location:
https://wormbase.org/tools/genome/jbrowse2/?session=share-YtcgDU0zgF&password=zju5Q
(that is, C. elegans N2, V:13707382..13707915)
and selecting "save track data" from the track ... menu, I get a dialog to save. GFF and BED don't really make sense in this context, so select GenBank (fasta would be a good option here too). The result looks like this:
Note the fractional coordinates:
V:13707382.014586711..13707915.014586711
. In some cases while look at this bug, I found that it also got the starting base wrong if the fraction was a little less than the starting coordinate (like it's doing aint
of the coordinate, which is not terribly unreasonable, but would be wrong in this case).Version:
JBrowse 2.6.3 (haven't had a chance to test with newer version yet) in Firefox
Additional context
The text was updated successfully, but these errors were encountered: