AltAnalyze version 2.0.3

[Nathan Salomonis]

We are pleased to announce the release of AltAnalyze 2.0.3
(http://www.altanalyze.org). This release provides several new
analysis features, including support of exon-level RNA-seq data (e.g.,
TopHat and BioScope), adjusted splicing p-values and normalization
methods, new annotations (NMD, alternative polyadenylation, direct
UniProt feature alignment), bug fixes and memory optimization. A new
file type is also introduced, which allows users to compare reciprocal
junction results to exon results, providing independent confirmation.
These new features are in more described here:
http://code.google.com/p/altanalyze/wiki/UpdateHistory
http://code.google.com/p/altanalyze/downloads/detail?name=AltAnalyze-Manual.pdf

In addition to these new features, we have updated several of the
program defaults, which will effect your results (e.g., default
RNA-seq normalization, gene expression thesholds and filters). Please
review these options when performing an analysis. Updates to
DomainGraph's database (Ensembl 62) should follow shortly. To see how
others are using AltAnalyze, view our citation page:
http://code.google.com/p/altanalyze/wiki/CitingArticles

As always, recommendation on how we can improve AltAnalyze are greatly welcome.

Best Regards,
AltAnalyze Development Team

http://www.altanalyze.org
http://code.google.com/p/altanalyze/
http://code.google.com/p/altanalyze/wiki/ContactUs

[Li, Haiqing]

Hi! Altanalyze development team,

I try to use the latest version 2.0.4 (windows 64bits), but got error:

Traceback (most recent call last):
File "AltAnalyze.py", line 5916, in <module>
File "AltAnalyze.py", line 5898, in runCommandLineVersion
File "AltAnalyze.py", line 5890, in cleanUpCommandArguments
IndexError: list index out of range

My OS is windows vista 64bits. And Both ver2.0.2 and ver2.0.3 work fine.

Any recommendations?

Thanks.

Haiqing

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[Nathan Salomonis]

Hi Haiqing,

At least one other user has reported a similar Windows configuration
that causes this error, although, the error does not occur on all
Windows 64 bit machines. The function causing this error is not useful
to AltAnalyze GUI users so I have made a simple change to the code
(placed an exception around this function) and re-posted 2.0.4 for
Win64. The live version will correct your issue.

Sorry for the inconvenience.

Best,
Nathan

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[Wanghua Li]

Hi! Altanalyze development team,
I am encountering the same problem with windows 32 bit machines for
AltAnalyzer version 2.0.4 as Haiqing. Some error information is in the
file AltAnalyze.exe.log:

Traceback (most recent call last):
File "AltAnalyze.py", line 5916, in <module>
File "AltAnalyze.py", line 5898, in runCommandLineVersion
File "AltAnalyze.py", line 5890, in cleanUpCommandArguments
IndexError: list index out of range

Could you help me and give me some addvice. Thank you very much!

Best wishes,
Wanghua Li

> > For more options, visit this group athttp://groups.google.com/group/alt_predictions?hl=en.- 隐藏被引用文字 -
>
> - 显示引用的文字 -

[Nathan Salomonis]

Hi Wanghua,

Thank you for letting us know that some 32bit users have the same issue. I will re-post the 32bit version when I am back in the office on Wednesday.

In the mean time, you can download the 64bit version, copy the files from the folder Source_code to the parent directory AltAnalyze_v.2.04 and run using by typing: python AltAnalyze.py in a command prompt when in this directory. If you get a warning that python is not installed, you will need to install python 2.7.1 and repeat.

Best,
Nathan

[Nathan Salomonis]

The live 32bit version now has that issue corrected.
Best,
Nathan