Up: Component summary
Up: Component summary
Component
FusionGenesAllows 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", |
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