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This page contains the necessary software to characterize mappability of RNA-Seq reads and create a "blacklist" of genomic positions of mismapped reads. This blacklist can be used to filter potential false positives from variant or RNA editing calls.
This software is described in "BlackOPs: Increasing Confidence in Variant Detection through Mappability Filtering" by CR Cabanski et al. Please cite this article if you use our software or available blacklists in your own analysis.
Features
- Perl scripts to create a custom blacklist
- Download existing blacklists for MapSplice and TopHat
- Detailed tutorial
- Detailed documentation
Follow BlackOPs: RNA-Seq Variant Blacklist Tool
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