Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction predictions, particularly in deep datasets with high coverage over splice sites.
In order to address this, instead for creating a new RNAseq mapper, with a focus on SJ accuracy we created a tool that takes in a BAM file generated by an RNAseq mapper of the user’s own choice (e.g. Tophat2, Gsnap, STAR2 or HISAT2) as input (i.e. it’s portable).
It then analyses and quantifies all splice junctions in the file before, filtering (culling) those which are unlikely to be genuine. Improving splice junction accuracy can help with many downstream tasks such as transcript reconstruction and differential splicing analysis.
GitHub
Documentation
http://portcullis.readthedocs.io/en/latest/