DOCUMENTATION
http://portal.nersc.gov/dna/RD/Adv-Seq/ALE-doc/
This code is no longer in active development. Pull requests and bugs will be addressed as needed.
Plotting
The authors recommend using IGV to view the output.
http://www.broadinstitute.org/igv/
Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.
LICENSE
/*
- Copyright (C) 2010,2011,2012 Scott Clark. All rights reserved.
-
- Developed by:
- Scott Clark
- Cornell University Center for Applied Mathematics
- http://cam.cornell.edu
- AND
- Rob Egan
- Department of Energy Joint Genome Institute
- http://jgi.doe.gov
-
- Permission is hereby granted, free of charge, to any person obtaining a
- copy of this software and associated documentation files (the "Software"),
- to deal with the Software without restriction, including without limitation
- the rights to use, copy, modify, merge, publish, distribute, sublicense,
- and/or sell copies of the Software, and to permit persons to whom the
- Software is furnished to do so, subject to the following conditions:
-
-
- Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimers.
-
- Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimers in the
- documentation and/or other materials provided with the distribution.
-
- Neither the names of Cornell University, The Joint Genome Institute,
- nor the names of its contributors may be used to endorse or promote
- products derived from this Software without specific prior written
- permission.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- DEALINGS WITH THE SOFTWARE.
*/
// For more information on the licence please see
// The University of Illinois/NCSA Open Source License
// http://www.opensource.org/licenses/UoI-NCSA.php
INSTALL
http://portal.nersc.gov/dna/RD/Adv-Seq/ALE-doc/index.html#installation
#
ALE comes packaged with samtools-0.1.18 Feel free to use a later version
samtools is open source (MIT license)
We would like to thank the creators for the extensive and very useful package
#
Requirements for plotter4.py:
numpy 1.6.1
mpmath 0.17
setuptools 0.6c11
matplotlib 1.0.1
pymix 0.8 http://www.pymix.org/pymix/