5d8f6cfeb71c1ce76dd992993eb4cabe65ebc73f dschmelt Wed Apr 17 09:52:26 2019 -0700 exanded descriptions for cdsStartStat/cdsEndStat #16081 diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index 11a77c5..cbba264 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -1064,32 +1064,32 @@ <pre><code>table genePredExt "A gene prediction with some additional info." ( string name; "Name of gene (usually transcript_id from GTF)" string chrom; "Chromosome name" char[1] strand; "+ or - for strand" uint txStart; "Transcription start position" uint txEnd; "Transcription end position" uint cdsStart; "Coding region start" uint cdsEnd; "Coding region end" uint exonCount; "Number of exons" uint[exonCount] exonStarts; "Exon start positions" uint[exonCount] exonEnds; "Exon end positions" int score; "Score" string name2; "Alternate name (e.g. gene_id from GTF)" - string cdsStartStat; "enum('none','unk','incmpl','cmpl')" - string cdsEndStat; "enum('none','unk','incmpl','cmpl')" + 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> <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"