b0d059aeeda703ccc16652a76cb0940921f4b462 brianlee Sun Jun 12 06:35:03 2022 -0700 Making Code Review changes refs #29553 diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index a67b3b3..4d911e2 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -1017,34 +1017,35 @@ 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; "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 values ('none','unk','incmpl','cmpl'). However, -the values are not used for our display and can not be used to subset for coding or non-coding -genes. For most purposes, to get more information about a transcript, other tables will need to -be used e.g. in the case of hg38, the tables named wgEncodeGencodeAttrsVxx, where xx is the +<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> <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"