Question: How To Convert Annotations In Embl Format To Gff Or Bed Format For Use In Igv?
gravatar for Tianyang Li
7.0 years ago by
Tianyang Li490
Beijing, China
Tianyang Li490 wrote:


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?


bed gff convert igv • 6.3k views
ADD COMMENTlink modified 6.9 years ago by Istvan Albert ♦♦ 80k • written 7.0 years ago by Tianyang Li490
gravatar for Istvan Albert
7.0 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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:

ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by Istvan Albert ♦♦ 80k

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).

ADD REPLYlink written 5.0 years ago by hpmcwill1.1k
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