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Under the terms of the GNU General Public License as published by the Free Software Foundation (version 3 or later) and No Warranty.


CrypSplice -C <A1.bed,..,An.bed> -T <B1.bed,..,Bn.bed> -G <MM10/HG19> -F <Read cutoff> -M <Junction match cutoff> -P <#of cores>


CrypSplice accepts junction quantifications in bed format

chr1 990 2099 JUNC00001560 872 + 990 2099 255,0,0 2 40,67 0,1042

chr2 101 2121 JUNC00001561 16 + 1010 2121 255,0,0 2 20,63 0,1048

-C Junction bed files of control samples

-T Junction bed files of treatment samples

Tip: If junction files are not in BED format consider using regtools to extract junctions in BED format.


-J Known Junctions data base in bed format.

-G Genome model directory containing respective alternativ splicing, gene model and Junction database files. Data for DM3, MM9, MM10 and HG19 are provided. For other genomes please download from UCSC genome browser.

Genome annotation related files including junction database (known junctions), known alternative splicing events and gene coordinates can be found in respective genome directories. If you are working with MM10 build: MM10-Known-SpliceJunctions.txt --> Junction database (Known junctions), MM10-Known-AE.txt --> Known splicing events and MM10.genes.bed ---> gene coordinates.

-F Minimum expression cutoff. Junctions with coverage less than this are ignored. Default 10.

-M Juntion match cutoff. To account sequencing errors junctions with reciprocal overlap of M or more are collapsed. Default 0.95 (95%).

-P Number of CPU cores to use. Default 1.


Bedtools V 2.17 or higher to be accessed from cmd line


R libraries ibb and MASS



CrypSplice also accommodates single sample data sets. However, we recommend users to use junction strength as a ranking metric.

To avoid confusion with multiple input files, we made -G parameter to handle all annotation related files. So if you provide -G you can ignore -J from earlier version.