Annotaion of complete and partial transposons in RNASeq

[gwilymh]

I am running an RNASeq analysis and am discovering new mRNA transcripts. Some of these transcripts seem to have homology with known transposable elements. I am currently assembling the new gene features into GFF3 files. Is there any recommended standard or protocol for labeling complete or partial transposons in this file format?

Are there any recommended standards, for example, to label the 'type' column (column 3)? In column 9, is there any widely used identifier for ID or Name or Ontology_term?

[GenoMax]

You could use the standard terms related to transposable elements: http://www.sequenceontology.org/brow...erm/SO:0000101

Description for the format is in Lincoln's post: http://www.sequenceontology.org/gff3.shtml