Sample files:        https://persephonesoft.com/data/import/AT.1-2.gff.gz , https://persephonesoft.com/data/import/human.bed

You can import annotations in GFF/GTF or BED formats. 

GFF files

When loading files in GFF format, you will be prompted to select the GFF types for import (as specified in column #3 of the file):

Select Genes to import "gene" or "mRNA" records. These are required to have either "exon" child records, or "CDS" child records (or both); "gene"/"mRNA" records without any children will be skipped. Select Other to import non-gene records, such as "repeat_masking" or "primer_match".

Qualifiers

If the input file contains "gene" or "mRNA" records, their qualifiers will be loaded as a standard flat table of qualifiers, and the annotation's Gene name will be inferred from fields in the input file (e.g. "Name" or "ID"). For example:

However, if the input file contains other records, e.g. mixed-strand primers, then their metadata will be imported as a single JSON block, and the annotation will remain unnamed. Click the button to expand the record and view individual fields:

BED files

Only the first three columns are required when loading BED files ("chrom", "chromStart", "chromEnd"). All other columns are optional, although "thickStart" and "thickEnd" (columns #7 and #8) will be ignored. The optional "itemRgb" field can be used to set annotation colors, and the "blockCount"/"blockSizes"/"blockStarts" fields are used to define exons. For example, the following file...

chr1        960103        965719        XM_006710600.3        0        +        960694        965191        0,100,250        12        698,260,122,222,186,214,145,168,89,74,182,757        0,1190,1526,1723,2183,2601,3006,3234,3817,4004,4246,4860
chr1        960103        963408        XM_006710601.3        0        +        960694        963312        250,100,250        7        186,214,377,698,260,122,222        2183,2601,2929,0,1190,1526,1723
chr1        960584        965719        NM_198317.3        0        +        960694        965191        100,100,250        12        217,260,122,222,117,214,145,168,89,74,182,757        0,709,1045,1242,1771,2120,2525,2753,3336,3523,3765,4379

...will produce the following annotations on an annotation track:

Persephone expands upon the official BED format by allowing HTML color codes and standard color names. For example:

chr1        960103        965719        XM_006710600.3        0        +        960694        965191        #ff0000        12        698,260,122,222,186,214,145,168,89,74,182,757        0,1190,1526,1723,2183,2601,3006,3234,3817,4004,4246,4860
chr1        960103        963408        XM_006710601.3        0        +        960694        963312        green        7        186,214,377,698,260,122,222        2183,2601,2929,0,1190,1526,1723
chr1        960584        965719        NM_198317.3        0        +        960694        965191        #99ccff        12        217,260,122,222,117,214,145,168,89,74,182,757        0,709,1045,1242,1771,2120,2525,2753,3336,3523,3765,4379