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SpliceGrapher - predicting splice graphs from diverse evidence Mark F. Rogers rogersma@cs.colostate.edu Version 0.2.4 released Description =========== SpliceGrapher is a Python-based scripting tool that uses gene models, RNA-Seq data and ESTs to predict splice graphs that capture in a single structure all the ways in which a gene's exons may be assembled. In a splice graph, a gene's exons are depicted as vertices and introns are depicted as edges between them. The compact structure allows researchers to visualize a gene's AS patterns more easily than by examining separate transcripts. SpliceGrapher includes modules that may be incorporated anywhere in an RNA-Seq analysis pipeline from initial alignment to final splice graph prediction. The package includes modules for constructing a database of known, recombined and predicted splice-junction sequences that may be used with ungapped short-read alignment algorithms such as MAQ, BowTie or PASS. The prediction modules are able to incorporate gene models in GFF3 format, RNA-Seq alignments in SAM format or EST alignments in PSL format. The viewing modules are able to read these same files to produce plots that depict a predicted graph along with the evidence SpliceGrapher used to produce it. Currently SpliceGrapher supports RNA-Seq alignments in SAM, BED and WIG formats, EST alignments in PSL format and Cufflinks transcript descriptions in GTF format. Installation ============ Only Unix/Linux/OS-X is supported. Requirements: matplotlib http://matplotlib.sourceforge.net (version 1.0.0 or higher) PyML http://sourceforge.net/projects/PyML (version 0.7.7 or higher) A setup.py script is provided so installation follows the standard python idiom: >>> python setup.py build >>> python setup.py install To install in a different directory than the system default, use >>> python setup.py install --home=/my/python/packages You may also install the stand-alone scripts in their own separate directory using the format: >>> python setup.py install --home=/my/python/packages --install-scripts=/my/python/scripts Updating paths ================== Before you run SpliceGrapher scripts, you will want to add the correct path to your PATH environment variable. By default this will be the /bin directory directly under the main installation directory. If you chose a different script path using the --install-scripts option, then use that path instead. If you used '--home=' to specify a home directory other than the default, you must ensure that it is included in your PYTHONPATH directory before you try to access SpliceGrapher's modules from python. Running Examples ================ The 'examples' subdirectory of the distribution contains example data and a shell script for creating splice graphs for the example data. To test your installation, simply run the script: >>> cd examples >>> run_tests.sh This script also provides examples to get you started using the SpliceGrapher Python scripts with your own data. Documentation ============= User Guide - doc/userguide.pdf Examples - SpliceGrapher/examples
Source: README, updated 2013-12-19