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Welcome to your wiki!
This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
The wiki uses Markdown syntax.
Feb 17 2013: This page under construction. Please return soon for updates including addition of perl scripts and detailed documentation and examples.
BlackOPs version 1.0.0 has been uploaded. The code can be downloaded as a zip folder under the Files tab, or the source code can be downloaded under the Code tab. Read the Tutorial for several examples showing how to run BlackOPs. More detailed documentation will be added.
You can also download existing blacklist files that were created and described in the accompanying manuscript (submitted). The blacklist positions are highly dependent on read length and alignment algorithm used. Therefore, if you use different parameters in your pipeline, we recommend that you do not use one of our files but that your create your own blacklist following the steps outlined in the Tutorial.
Last edit: Chris Cabanski 2013-03-21
BlackOPs version 1.0.1 has been uploaded. This version contains documentation for all perl scripts. Minor inconsistencies between the tutorial and perl scripts were also fixed.
BlackOPs version 1.0.2 has been uploaded. This version includes a new perl script, insert_errors.pl, that randomly inserts sequencing errors (base substitutions) into the simulated reads. The error rate can be set by the user.
Our manuscript describing BlackOPs has been published by Nucleic Acids Research. If you use our software or available blacklists, please cite
Cabanski CR, Wilkerson MD, Soloway M, Parker JS, Liu J, Prins J, Marron JS, Perou CM, Hayes DN. (2013) BlackOPs: Increasing Confidence in Variant Detection through Mappability Filtering. Nucleic Acids Research. doi:10.1093/nar/gkt692.
BlackOPs version 1.0.3 has been uploaded. The only changes in this new version are in the tutorial, where we updated the citation information.
Last edit: Chris Cabanski 2013-08-09
BlackOPs version 1.0.4 has been uploaded. This fixes a bug in get_ref_transcript.pl and get_ref_exon.pl that was not correctly taking the reverse complement of sequences containing lower case letters (a,c,g,t).
BlackOPs version 1.0.5 has been uploaded. Many users were experiencing problems recreating accurate transcript sequences using get_ref_transcript.pl and get_ref_exons.pl. These problems were often a result of using a reference genome that contained line breaks and header lines. The tutorial was modified to more clearly mention that the reference genome should not contain line breaks and provide a simple Unix command to remove line breaks.