Up: Component summary
Up: Component summary
Function
AnnotEnsemblTakes the ncRNA fasta file downloaded from Ensembl and creates a gff file with the transcript IDs as the reference chromosome. This is required for alignment of reads to ncRNAs in Ensembl.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Annotation smallRNA |
| Authors | Katherine Icay (katherine.icay@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | biomaRt (R-package) ; Biostrings (R-package) |
| Source files | component.xml function.scala |
| Usage | Example with default values |
Outputs| Name | Type | Description |
|---|---|---|
| annot | CSV | Key-File CSV file containing the path to the modified GFF3 file. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| ensembl_dataset | string | "hsapiens_gene_ensembl" | biomaRt dataset parameter (i.e. species) to use. |
| ensembl_host | string | "feb2014.archive.ensembl.org" | URL of Ensembl version to use (see Ensembl Archives). To guarantee optimal identification of transcripts, be sure to use the same genome build AND version of the genome as reference_hairpin. |
| reference | string | "" | Path to Ensembl fasta file of known and novel ncRNA sequences. Required for the function to work! |