CAP3 is a contig assembly program. It allows to assembly long DNA reads (up to 1000 bp). Binaries can be downloaded from http://seq.cs.iastate.edu/cap3.html Huang, X. and Madan, A. (1999) CAP3: A DNA Sequence Assembly Program, Genome Research, 9: 868-877.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Output file | Select which type of genes need to output. up for genes upstream to peak summit, down for genes downstream to peak summit, all for both up and down. (--op). | all |
| Quality cutoff for clipping | Output official gene symbol instead of refseq name. (--symbol). | False |
| Clipping range | Set a number which unit is base. It will get the refGenes in n bases from peak center. (--distance). | 3000 |
| Quality cutoff for differeneces | ||
| Maximum difference score | ||
| Match score factor | ||
| Masmatch score factor | ||
| Gap penalty factor | ||
| Overlap similarity score cutoff | ||
| Overlap length cutoff | ||
| Overlap percent identity cutoff | ||
| Max number of word matches | ||
| Band expansion size | ||
| Max gap length in an overlap | ||
| Assembly reverse reads | ||
| CAP3 tool path | ||
| Temporary directory |
Parameters in Workflow File
Type: peak2gene-id
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| genome | Genome file | string |
| outpos | Output file | string |
| symbol | Official gene symbols | boolean |
| distance | Distance | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: Peak2gene data
Name in Workflow File: in-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Treatment features | _treat-ann | ann-table-list |
And 1 output port:
Name in GUI: Peak2gene output data
Name in Workflow File: out-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Gene regions | gene-annotation | ann-table-list |
| Peak regions | peak-annotation | ann-table-list |