-
Notifications
You must be signed in to change notification settings - Fork 1
Reference: How is my reference supposed to be formatted or formulated?
marabouboy edited this page Dec 13, 2021
·
3 revisions
I will show what type of reference files are accepted and examples of how the GTF files are required to be formatted/formulated
1. GFF/.gff3 format:
2. Conversion into GTF/.gtf format:
- While you could use another open-source or propreitary software when converting the GFF3-file into a GTF-file, the FLAME program is deigned with using the Galaxy web-based platform in mind. Using the standardized format is planned to be integrated into the FLAME program.
- My recommendation is to upload the GFF3 file into Galaxy
- Following uploading the GFF3 file, using the
gffread
function, with the important parameters highlighted in red: - Ideally, your GTF annotation reference file should resemble or be formated like this:
3. Adding additional exons to your reference:
- Once you have cycled through FLAME once and have one or several novel exons suggested, to add the novel exons to the GTF annotation reference file, one simply needs to manually add an additional line in the GTF-file with all but the exon starting and ending position being altered. Remember to also specify that the added novel exon is "
exon
" and not "CDS
" in the third column as the CDS are automatically filtered out in the FLAME workflow. - Ideally, your additional exon follows this format, with the novel exons highlighted in red: