Up: Component summary
Up: Component summary
Function
FusionMapDetect genomic fusions from paired or single ended DNA-seq or RNA-seq data using FusionMap. FusionMap works by splitting reads into three parts, aligning the prefix and suffix reads, and detecting fusions by discordant alignment of the prefix and suffix. The most important parameters are minSeedLength (alpha) and maxAlignments (beta).
Notes: FusionMap 7.0.1.25 does not appear to work with Mono 3+, so Mono 2.10.9+ should be used. On the first run, FusionMap may take a long time at "Thread number=N"; this is due to downloading and processing of the genome index.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Short-read Sequencing |
| Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | FusionMap ; Mono (2.10.9+ or 2.11) |
| Source files | component.xml function.scala |
| Usage | Example with default values |
| Deprecated |
We have FusionCaller component. |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| reads | RegionSet | Mandatory | Sequencing reads in FASTQ/FASTA/BAM format (optionally gzipped). Data can either include all reads, or only unmapped reads after an initial alignment; the latter reduces FusionMap run time. |
| mates | RegionSet | Optional | For paired-end sequencing, these are the mate reads in the same format as primary reads. |
Outputs| Name | Type | Description |
|---|---|---|
| fusions | CSV | Fusion table. See column descriptions. |
| fusionReads | BAM | Fusion reads. Each read has been cut into two parts, which align to different locations. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| fusionMapPath | string | "" | Path to FusionMap installation, i.e., the directory that contains bin as a subdirectory. This directory must be writable by the user. If the parameter is empty, the environment variable FUSIONMAP_HOME is used. |
| geneModelName | string | "Ensembl.R73" | Code of the gene model in Array Suite nomenclature. Only used for RNA-seq. |
| maxAlignments | int | 1 | Maximum number of read end alignments (beta in the FusionMap article). Range: 1 to 5. |
| memoryGB | int | 8 | An estimate for memory usage by FusionMap. Only used in a cluster environment. For the human genome, 7-8 GB are needed. |
| minSeedLength | int | 25 | Minimum length of a seed read (alpha in the FusionMap article). If 0, the length is computed using Min(25, Max(17,floor(ReadLength/3))). |
| mismatchPercentage | int | 8 | Percentage (0 to 100) of allowed mismatches in alignment of reads. |
| monoExec | string | "" | Path to Mono executable, if not on path. Example: /opt/mono/bin/mono. |
| referenceName | string | "Human.B37.3" | Code of the reference genome in Array Suite nomenclature. |
| rna | boolean | true | If true, data are from RNA-seq. If false, data are from genomic DNA-seq. |
| threads | int | 4 | Number of threads used by FusionMap. |
Test cases| Test case | Parameters▼ | IN reads |
IN mates |
OUT fusions |
OUT fusionReads |
|
|---|---|---|---|---|---|---|
| case1_pe | (missing) | reads | mates | fusions | (missing) | |
| case2_se | properties | reads | (missing) | fusions | (missing) | |
|
rna=false |
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