Command-line reference

Every splicekit invocation prints its version first, then runs the requested command. Run splicekit -help for the built-in summary; this page is the fuller reference.

Processing

Command	Description
splicekit process	Run all available analyses in order: setup, annotation, features, edgeR, juan, judge, motifs, promisc, clusterlogfc, june, report, jbrowse2.

Initialization

Command	Description
splicekit setup	Initialize the project folder structure.
splicekit annotation	Load samples.tab and build comparisons. See Sample annotation.
splicekit features	Create junction/exon/anchor/gene count tables from BAM files. See Features & count tables.

Splicing analyses

Command	Description
splicekit edgeR [junctions\|exons\|anchors\|genes]	Run edgeR differential usage analysis. All feature types if no sub-command is given. See Differential splicing (edgeR).
splicekit dexseq [junctions\|exons\|anchors\|genes]	Run DEXSeq as an alternative to edgeR. See Additional analyses.
splicekit juan	Merge donor/acceptor anchor edgeR results into the junction results.
splicekit judge	Generate juDGE plots (junction logFC vs. gene logFC). See juDGE plots.
splicekit promisc	Promiscuity analysis: genes and their junction changes across conditions.
splicekit clusterlogfc	Cluster comparisons by logFC of significant (FDR < 0.05) changes, at junction/exon/gene level.
splicekit june	JUNE junction-event analysis (e.g. skipped/mutually exclusive exons).
splicekit rmats	Process the project's BAM files with rMATS.
splicekit cassettes	Cassette exon analysis.
splicekit patterns	Sequence pattern analysis.

Motif & scanRBP

Command	Description
splicekit motifs [dreme\|scanrbp]	Run motif logos, DREME and scanRBP analysis. All three if no sub-command is given. See Motif & RNA-binding analysis.

JBrowse2 & reporting

Command	Description
splicekit jbrowse2 [process\|start]	Process (build) JBrowse2 files and/or start the JBrowse2 web server. Both steps if no sub-command is given.
splicekit jbrowse	Alias for splicekit jbrowse2.
splicekit web	Start the local web server serving both the HTML report and JBrowse2. See Exploring results.
splicekit report	Generate the HTML report under report/.

Other

Command	Description
splicekit version	Print the installed splicekit version.

Global options

Option	Description
-help	Print the built-in usage summary (or a sub-command's usage, e.g. splicekit edgeR -help).
-version	Print the installed version and exit.
-verbose	Print more detailed progress output.
-force	Force recomputation of steps that would otherwise be skipped if their output already exists (used by process and jbrowse2).