6218aa92f1135a9cae1423439ddf13dddd65655e max Fri Apr 21 03:27:45 2023 -0700 #Preview2 week - bugs introduced now will need a build patch to fix fix typos in last commit diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index ecdbbfc..d45f60d 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -3,31 +3,31 @@ <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Frequently Asked Questions: Gene tracks</h1> <h2>Topics</h2> <ul> <li><a href="#gene">What is a gene?</a></li> <li><a href="#genestrans">What is a transcript and how is it related to a gene?</a></li> <li><a href="#genename">What is a gene name?</a></li> <li><a href="#mostCommon">What are the most common gene transcript tracks?</a></li> <li><a href="#wrong">I think this transcript looks strange, what shall I do?</a></li> -<li><a href="#duplicate">Why does the UCSC refGene track include duplicates, where a transcript maps to two places?</a></li> +<li><a href="#duplicates">Why does the UCSC RefSeq track ("refGene") include duplicates, and some transcripts map to two loci?</a></li> <li><a href="#ens">What are Ensembl and GENCODE and is there a difference?</a></li> <li><a href="#ensRefseq">What are the differences among GENCODE, Ensembl and RefSeq?</a></li> <li><a href="#hg19">For the human assembly hg19/GRCh37: What is the difference between "UCSC Genes" track, the "GENCODE" track and the "Ensembl Genes" track?</a></li> <li><a href="#hg38">For the human assembly hg38/GRCh38: What are the differences between the "GENCODE" and "All GENCODE" tracks?</a></li> <li><a href="#gencode">What is the difference between GENCODE comprehensive and basic?</a></li> <li><a href="#ncbiRefseq">What is the difference between "NCBI RefSeq" and "UCSC RefSeq"?</a></li> <li><a href="#mito">What is the best gene track for mitochondrial gene annotations?</a></li> <li><a href="#report">How shall I report a gene transcript in a manuscript?</a></li> <li><a href="#ccds">What is CCDS?</a></li> <li><a href="#justsingle">How can I show a single transcript per gene?</a></li> <li><a href="#singledownload">How can I download a file with a single transcript per gene?</a></li> <li><a href="#whatdo">This is rather complicated. Can you tell me which gene transcript track I should use?</a></li> @@ -197,31 +197,31 @@ </tr> </table> <a name="wrong"></a> <h6>I think this transcript looks strange, what shall I do?</h6> <p>The Genome Browser Group only displays transcripts provided by others. But both RefSeq and Gencode have dedicated staff that look manually at each and every transcript and they know everything there is to know about gene models. They are happy to answer your questions and they can change the transcript annotation. Submit your questions via the <a href="https://www.ncbi.nlm.nih.gov/projects/RefSeq/update.cgi" target=_blank>RefSeq contact form</a> or the <a href="https://www.gencodegenes.org/pages/contact.html" target=_blank>Gencode context form.</a> </p> <a name="duplicates"></a> -<h6>Why does the UCSC RefSeq track ("refGene") include duplicates, and some transcripts map to two places?</h6> +<h6>Why does the UCSC RefSeq track ("refGene") include duplicates, and some transcripts map to two loci?</h6> <p>This is related to the question <a href="#ncbiRefSeq">What is the difference between "NCBI RefSeq" and "UCSC RefSeq"?</a> below. Briefly, the UCSC refGene track aligns the RefSeq transcripts to the genome with BLAT, with no special filtering but a 95% identity, the NCBI RefSeq track is NCBI's mapping and the NCBI alignments were filtered using manual annotations to make sure that a transcript is mapped only once, even if it is perfectly aligning twice. NCBI uses manual curation to decide on the best placement, for example, if a gene is annotated on chr4, any alignments, even 100% identical, from other chromosomes are removed. As a result, the UCSC RefSeq track contains duplicates if the transcripts align very well to both loci and alerts the user to this fact, where as the NCBI alignments were filtered manually to make sure that every transcript maps only once. </p> <a name="ens"></a> <h2>The differences</h2>