KisSplice

A local transcriptome assembler for SNPs, indels and AS events

KisSplice2refgenome

KisSplice can also be used when a reference (annotated) genome is available, in order to annotate the variants found and help prioritize cases to validate experimentally.
In this case, the results of KisSplice are mapped to the reference genome, using gmap or STAR, and the mapping results are analysed using KisSplice2RefGenome.
Ultimately, for each variant, KisSplice2RefGenome outputs : a gene name, the type of event, CDS/UTR/intergenic, frameshift?, deltaPSI... and other technical features which may be useful for automatic post-treatment.
By default, the results are ranked by decreasing deltaPSI.
A short tutorial explaing how to run KisSplice, STAR and KisSplice2refGenome is available here
The full protocol from our SR paper is available here

Version 1.2.3

kissplice2refgenome version 1.2.3 (2019-08-27)
User's guide

Changelog

This is a bug-fixing update:

  • The number of annotated splices sites was not correctly reported for the following event types: Intron Retention, Insertion and Deletion

Version 1.2.2

kissplice2refgenome version 1.2.2 (2019-07-20)
User's guide

Changelog

This is a bug-fixing update:

  • The CDS column is now correctly reported if the AS event is located within the CDS of a gene. This is useful for prioritising candidates;

Version 1.2.1

kissplice2refgenome version 1.2.1 (2018-08-20)
User's guide

Changelog

This is a bug-fixing update:

  • Corrected the parsing of the CIGAR string in unmapped events;

Version 1.2.0

kissplice2refgenome version 1.2.0 (2018-07-13)
User's guide

Changelog

This is a bug-fixing update:

  • Corrected the bubble clustering;

Version 1.1.0

kissplice2refgenome version 1.1.0 (2018-04-10)
User's guide

Changelog

This is a bug-fixing/performance update:

  • More precise event calling;
  • Corrected a bug with the strand column;
  • Improved performance.

Version 1.0.0

kissplice2refgenome version 1.0.0 (2015-05-11)
User's guide

Requirements

KisSplice2refgenome requires Python 2.7.x and works on Linux systems. It requires

It is necessary to have as an input a file coming from the mapping of KisSplice results against a reference genome. KisSplice2refgenome allows .psl and .sam formats. For annotation files, .gtf is accepted.

Using kissplice2refgenome

You have access to all options description with the help command :

kissplice2refgenome -h

A first and very simple way to use KisSplice2refgenome is to input only the mapping file (psl or sam). An annotation (gtf) can also be added.

kissplice2refgenome <MAPPING_OUTPUT> -a [AnnotationFile] -o [PathToWriteOutput]