Up: Component summary
Up: Component summary
Component
GetUtrSeqFetch UTR sequences of query transcripts. It can support both 5' and 3' UTRs.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | smallRNA |
| Authors | Ping Chen (ping.chen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | Ensembl Perl API |
| Source files | component.xml GetUtrSeq.pl |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| transcripts | CSV | Mandatory | Transcript Ensembl IDs. |
| connection | Properties | Mandatory | Connection parameters of Ensembl database, including host, database, port, user and driver information. |
Outputs| Name | Type | Description |
|---|---|---|
| UTR5 | FASTA | 5' UTR sequences in FASTA format. |
| UTR3 | FASTA | 3' UTR sequences in FASTA format. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| primeType | string | "3prime" | The type of UTR regions to be fetched. It could be one of '5prime', '3prime' or both. |
Test cases| Test case | Parameters▼ | IN transcripts |
IN connection |
OUT UTR5 |
OUT UTR3 |
|---|---|---|---|---|---|
| case1 | (missing) | transcripts | connection | UTR5 | UTR3 |