Blacktie: a streamlined interface to the popular tophat/cufflinks RNA-seq pipeline
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README.rst

Welcome to Blacktie!

This package is functional but under heavy development so you may want to periodically pull the latest code from the repo at git://github.com/xguse/blacktie.git.

For the LATEST version pull the 'develop' branch.

I seek collaboration and contributions to improve this tool.

PLEASE take it and run with it, but send me your progress!

Its goal is to simplify the integration of all the input/output streams of the tophat/cufflinks workflow into a single yaml based config file and automate as much of everything else as possible so that once the config file is filled out, the entire process of analyzing a multi-condition RNA-seq experiment can be run with a single command.

Documentation

Current version of the docs can be found here: https://blacktie.readthedocs.org/en/latest/

Issue tracking

If you find issues, bugs, or have feature requests, please go here to submit them: https://github.com/xguse/blacktie/issues

Blacktie Poster

To credit the use of blacktie please cite the poster using the DOI link provided.

Introducing Blacktie: a simpler way to do RNA-seq using Tophat/Cufflinks/CummeRbund. Augustine Dunn. figshare. http://dx.doi.org/10.6084/m9.figshare.714149

Credits

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