Comments (6)
AltAnalyze has not been tested yet on Mac OS 10.9.1, however, we have received
other reports of incompatibility with this OS. We expect to upgrade at least
one test machine to this OS in early February in coordination with our IT
department.
In the meantime, I recommend either running AltAnalyze from source code and
installing necessary dependencies described here:
http://code.google.com/p/altanalyze/wiki/StandAloneDependencies
Alternatively, you can install a desktop virtual app, such as VirtualBox with
Windows or Ubuntu 12.04 and run the compiled AltAnalyze version there.
Original comment by [email protected]
on 13 Jan 2014 at 9:05
from altanalyze.
Thanks for the reply. I tried running it through a virtualbox Linux Ubuntu
12.04 installation on my Mac, and have the same issue. Originally the program
worked, but wouldn't "Add New Species". After I chose a species from the
server, the program did allow me to attempt to "Add New Species" but crashed
after I gave the species name and now won't run at all. Now when I click on
"begin analysis" it crashes.
Please help.
Original comment by [email protected]
on 15 Jan 2014 at 2:42
from altanalyze.
Does it work if you just select a species to download? What species are you
trying to add? What kind of data is this?
The species addition is only useful if you want to manually create a species
database outside of AltAnalyze, and really only that is useful for non-splicing
analyses. My recommendation is that if AltAnalyze works fine on Mac or Ubuntu
with a downloaded species and if you have gene/metabolite/proteomics data for a
non-supported species, just download the Zea Mays database (smallest in size),
pick "Other" as your system and any of the ID systems shown below and proceed
with your analysis. This will give you all of the basic statistical and
comparison analyses, including MarkerFinder, PCA, hierarchical clustering and
other QC, but won't add any annotations to your data.
Original comment by [email protected]
on 15 Jan 2014 at 3:09
from altanalyze.
My goal is to run splicing analysis on RNA-seq data from the purple sea urchin
(S. purpuratus), that has a genome and gff annotation files from cufflinks /
publications. If it's not possible to perform splicing analysis with a "New
Species" then I will need to look elsewhere for another application, correct?
Original comment by [email protected]
on 15 Jan 2014 at 3:22
from altanalyze.
My goal is to run splicing analysis on RNA-seq data from the purple sea urchin
(S. purpuratus), that has a genome and gff annotation files from cufflinks /
publications. If it's not possible to perform splicing analysis with a "New
Species" then I will need to look elsewhere for another application, correct?
Original comment by [email protected]
on 15 Jan 2014 at 3:59
from altanalyze.
Although it has been on our action item list add support for the Ensembl
bacterial, metazoan, etc. websites, which will just require some tweaking to
our update code to allow for this different build sites, we haven't yet.
If you are python friendly I can tell you how to do this on a species by
species basis, but otherwise it won't be available for the new few months at
least.
Best,
Nathan
Original comment by [email protected]
on 15 Jan 2014 at 6:22
from altanalyze.
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