Up: Component summary Function


Takes 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)
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Requires biomaRt (R-package) ; Biostrings (R-package)
Source files component.xml function.scala
Usage Example with default values


Name Type Description
annot CSV Key-File CSV file containing the path to the modified GFF3 file.


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!

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