96c296bf6fcb45403903e0768b48126c634a83de max Tue Jun 3 14:09:56 2025 -0700 small changes to FAQformat, after call with Brian, no redmine diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index ad9451a03d4..09adecd6a4e 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -1033,37 +1033,40 @@ string name2; "Alternate name (e.g. gene_id from GTF)" string cdsStartStat; "Status of CDS start annotation (none, unknown, incomplete, or complete)" string cdsEndStat; "Status of CDS end annotation (none, unknown, incomplete, or complete)" lstring exonFrames; "Exon frame offsets {0,1,2}" ) </code></pre> <p>The fields cdsStartStat and cdsEndStat can have the following values: 'none' = none, 'unk' = unknown, 'incmpl' = incomplete, and 'cmpl' = complete. However, the values are not used for our display and cannot be used to identify which genes are coding or non-coding. For most purposes, to get more information about a transcript, other tables will need to be used. For instance, in the case of hg38, the tables named wgEncodeGencodeAttrsVxx, where xx is the Gencode Version number. See this <a href="../../FAQ/FAQgenes.html#coding" target="_blank">coding/non-coding genes FAQ</a> for more information.</p> <p> -The field <code>exonFrames</code> is a comma-separated list of the numbers +<b>The exonFrames field:</b> The field <code>exonFrames</code> is a comma-separated list of the numbers with the possible values 0, 1, 2 or -1, one per exon, in order of transcription. -This order means that the first value for a transcript on the minus (-) strand is +This is different than the exonStarts and exonEnds fields - if the transcript is on the negative strand, +exonFrames are in the reverse order relative than exonStarts. +Put differently, it means that the first value for a transcript on the minus (-) strand is the exon on the right of the screen on the Genome Browser. A value of zero means that the first codon of the exon starts at the first nucleotide of the exon. A value of one means that the first codon starts after the first nucleotide and a value of two means that it starts after the second nucleotide. +See also our <a href="../../goldenPath/help/codonPhase.html">phase documentation</a>. UTRs are non-coding and their exonFrame value is -1.</p> <a name=RefFlat></a> <p><strong>Gene Predictions and RefSeq Genes with Gene Names</strong></p> <p> A version of genePred that associates the gene name with the gene prediction information. In alternative-splicing situations, each transcript has a row in this table.</p> <pre><code>table refFlat "A gene prediction with additional geneName field." ( string geneName; "Name of gene as it appears in Genome Browser." string name; "Name of gene" string chrom; "Chromosome name" char[1] strand; "+ or - for strand" uint txStart; "Transcription start position"