transcript/gene file
A transcript/gene file is a tsv file
containing a list of transcripts. Each line contains one transcript.
The standard region fields (chromosome, begin and end) indicate the
location of the transcript (and the transcript file is thus also a
region file) while other fields indicate the strand, exons etc.
The basic fields for a transcript file are
- chromosome
- chromosome name
- begin
- transcription start position
- end
- transcription end position
- strand
- indication of the strand; + or -, empty or . can be used for
unknown
- exonStarts
- list of exon start positions
- exonEnds
- list of Exon end positions
- cdsStart
- start of the coding region (genomic position)
- cdsEnd
- end of the coding region (genomic position)
- transcript
- Name of transcript (usually transcript_id from GTF)
- gene
- name of gene. This field preferentially contains the HGNC
name for the gene, but other ids are possible
- geneid
- This field typically contains the id of a gene (e.g. ensembl
id for gene)
Most genomecomb tools will accept some (commonly encounterd)
alternative fieldnames if these are not present:
- chromosome
- "chrom", "chr", "chr1",
"genoName", "tName" and "contig"
- begin
- "start", "end1", "chromStart",
"genoStart", "tStart", txStart",
"pos" and "offset" (end1 is recognised as begin
because of the structural variant code in genomecomb, where
start1,end1 and start2,end2 regions surround a SV).
- end
- "start2", "chromEnd",
"genoEnd", "tEnd" or "txEnd"
- transcript
- "transcript_id", "transcriptid",
"name"
- gene_name
- "gene","name2", "geneid",
"gene_id"
Any other fields can be added, but the following are common:
- category
- field indicating if the transcript is known, novel or
intergenic (transcript of a novel gene); for novel transcripts how
they differ from (the closest) known transcipt can be added after
novel (, e.g. novl_in_catalog)
- exonCount
- number of exons
- source
- source of data
- geneid
- a gene identifier, such as the ensembl id. This field can be
used to add a specific id as well as the HGNC name (in gene).
Genomecomb also checks the fields
"gene_id","gene_name","gene",
"name2" for this. Remark that these alternative field
names overlap with gene alternatives. This provides for when no
specific gene id was provided.