4. GS De Novo Assembler and GS Reference Mapper Appendices
:
4.10 Annotation File Formats
: 4.10.2 refGene.txt File Format
4.10.2
refGene.txt File Format
The Golden Path file refGene.txt is a tab-delimited text file consisting of 16 fields. All fields are required, including the bin field. The value of the bin field is ignored, but must be present.
Field
Description
bin
Indexing field
name
Name of gene
chrom
Reference sequence chromosome or scaffold
strand
+ or - for strand
txStart
Transcription start position
txEnd
Transcription end position
cdsStart
Coding region start position
cdsEnd
Coding region end position
exonCount
Number of exons
exonStarts
Comma-separated list of exon start positions
exonEnds
Comma-separated list of exon end positions
id
Unique identifier
name2
Alternate name
cdsStartStat
'none', 'unk', 'incmpl' or 'cmpl'
cdsEndStat
'none', 'unk', 'incmpl' or 'cmpl'
exonFrames
Exon frame offsets {0,1,2}