TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Output directory | Directory to save MACS output files. | |
| Bowtie index directory | The directory with the Bowtie index for the reference sequence. | |
| Bowtie index basename | The basename of the Bowtie index for the reference sequence. | |
| Mate inner distance | The expected (mean) inner distance between mate pairs. | Standart Illumina |
| Mate standard deviation | The standard deviation for the distribution on inner distances between mate pairs. | |
| Library type | Specifies RNA-Seq protocol. | False |
| No novel junctions | Only look for reads across junctions indicated in the supplied GFF or junctions file. This parameter is ignored if Raw junctions or Known transcript file is not set. | 0.1 |
| Raw junctions | The list of raw junctions. | |
| Known transcript file | A set of gene model annotations and/or known transcripts. | 0.15 |
| Max multihits | Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many alignments. | default |
| Segment length | Each read is cut up into segments, each at least this long. These segments are mapped independently. | default |
| Fusion search | Turn on fusion mapping. | |
Parameters in Schema File
Type: cufflinks
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| out-dir | Output directory | string |
| ref-annotation | Bowtie index directory | string |
| rabt-annotation | Bowtie index basename | string |
| library-type | Mate inner distance | numeric |
| mask-file | Mate standard deviation | string |
| multi-read-correct | Library type | boolean |
| min-isoform-fraction | No novel junctions | numeric |
| frag-bias-correct | Raw junctions | string |
| pre-mrna-fraction | Known transcript file | numeric |
| path | Max multihits | string |
| tmp-dir | Segment length | string |
| Fusion search | ||
Input/Output Ports
The element has 1 input port:
Name in GUI: Input reads
Name in Schema File: in-assembly
Slots:
| Slot In GUI | Slot in Schema File | Type |
|---|---|---|
| Assembly data | assembly | assembly |
| Source url | url | string |
And 1 output port:
Name in GUI: Output annotations
Name in Schema File: out-annotations
Slots:
| Slot In GUI | Slot in Schema File | Type |
|---|---|---|
| Isoform-level expression values | isolevel.slot | ann_table |