Up: Component summary Function

AnnotMirbase

Takes a GFF3 file downloaded from miRBase and modifies the genomic locations to reference by Ensembl transcript ID (instead of chromosome) and relative positions inside the transcript ID (start and end positions). The output is then used as the input reference for HTSeq-count.

Version 1.0
Bundle sequencing
Categories Annotation smallRNA
Authors Katherine Icay (katherine.icay@helsinki.fi)
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Requires biomaRt (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
annotation_mirbase string "" Path to downloaded miRBase GFF3 file. Required for the function to work!
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_hairpin string "" Path to Ensembl fasta file of known smallRNA sequences. Required for the function to work!

Test cases

Test case Parameters OUT
annot
case1 properties annot

annotation_mirbase=../../../sequencing/functions/AnnotMirbase/testcases/case1/annotation_mirbase.gff3,
reference_hairpin=../../../sequencing/functions/AnnotMirbase/testcases/case1/reference_hairpin.fa,
ensembl_host=dec2013.archive.ensembl.org


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