How To Convert Annotations In Embl Format To Gff Or Bed Format For Use In Igv?

Question

[Tianyang Li]

Hi,

I have some annotations that I downloaded which are in EMBL format.

Right now I'd like to view it in IGV, and I read that I must get the annotations in GFF or BED format first.

I've tried converting EMBL to GenBank format, then to GFF, but IGV didn't show any annotations.

Does anybody have related previous experiences?

Thanks!

Answer 1

[Istvan Albert]

Make sure that it is in the GFF3 format, and that it also contains the header pragma:

##gff-version   3

Edit: you can also convert directly via: http://www.ebi.ac.uk/cgi-bin/readseq.cgi

[hpmcwill]

Also see Converting Gff/Gtf + Reference To Embl Or Genbank ...Any Tools Available? for examples of converting EMBL-Bank format to GFF using EMBOSS seqret. Please note these examples use GFF version 2 (gff), for GFF version 3 use the feature format name 'gff3' instead of 'gff' (see A.2. Supported Feature Formats for details of the various sequence feature formats supported by EMBOSS).