Up: Component summary Component

FusionGenes

Allows filtering of alignments in BAM/SAM files, mainly output from Tophat

Version 1.0
Bundle sequencing
Categories
Authors Alejandra Cervera (alejandra.cervera@helsinki.fi)
Issue tracker View/Report issues
Requires TopHat ; installer (bash)
Source files component.xml runFusion.sh
Usage Example with default values
Deprecated

This component is not being used anymore, we have FusionCaller component.

Inputs

Name Type Mandatory Description
in Array<BinaryFolder> Mandatory An array with the output folders of the TopHat runs. Each folder should contain the accepted_hits.bam file plus the other files that TopHat produces when run on fusion search mode.

Outputs

Name Type Description
out BinaryFolder A SAM file filtered.

Parameters

Name Type Default Description
annotationsDir string (no default) A folder that contains the required annotations for TopHat fusion (ensGene.txt, refGene.txt, blast database). Since these files need to be in the same directory where the alignments are, a hard link is created from these files to the execution directory. This means that the files have to be in the same filesystem as the execution directory.
options string "-p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5" Parameters for tophat-fusion-post.
referenceDir string (no default) The reference genome along with Bowtie index files.

Test cases

Test case Parameters IN
in
OUT
out
case1 properties in (missing)

annotationsDir="/mnt/csc-cloud/resources/tophat-fusion-post",
referenceDir="/mnt/csc-cloud/resources/references_annotations/Ensemblv70/CHR/Sequence/BowtieIndex/genome"


Generated 2018-12-17 07:42:22 by Anduril 2.0.0