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.

Mappers

KisSplice2RefGenome takes as input a .psl or .sam file. This can be obtained using many mappers. We have tested STAR and gmap. For a first use, we recommend STAR, because it is fast, annotation-aware (using -sjdb* options) and still discovers novel exon junctions.
By default, STAR outputs only the best match for each variant. This can be changed for an advanced usage. If the focus is on indels of size >5, the gap extension penalty should be changed, otherwise STAR will filter them out.
If RAM is a limiting factor, then gmap gives also good results. Its limitations are that it does not use annotations, hence relies on GT-AG consensus to identify introns. By default, it outputs also suboptimal matches. This will result in a bubble having several locations assigned to it in the final result file.

In any case, whatever the mapper used, we take advantage of the fact that both variants of the bubble should be mapped to the same location. This helps in discarding spurious mappings.
Bubbles for which the variants could not be mapped to the same genomic location are reported in an independent log file.

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]