0c04b1cdeb2453a69da42683252e4285d0838362 lrnassar Thu Jul 4 11:38:28 2019 -0700 Expanding transMap data access section #23629 diff --git src/hg/makeDb/trackDb/transMapTailer.html src/hg/makeDb/trackDb/transMapTailer.html index 5ddcb79..ca53275 100644 --- src/hg/makeDb/trackDb/transMapTailer.html +++ src/hg/makeDb/trackDb/transMapTailer.html @@ -66,31 +66,34 @@ location and is given the identifier <tt>BC149621.1-1.1</tt>. However, <tt>BC149621.1-2</tt> maps to two locations, resulting in <tt>BC149621.1-2.1</tt> and <tt>BC149621.1-2.2</tt>. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. </P> <h2>Data Access</h2> <p> The raw data for these tracks can be accessed interactively through the <a href="hgTables">Table Browser</a> or the <a href="hgIntegrator">Data Integrator</a>. For automated analysis, the annotations are stored in <a href="../goldenPath/help/bigPsl.html">bigPsl</a> files (containing a number of extra columns) and can be downloaded from our -<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/transMap/">download server</a>. +<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/transMap/">download server</a>, +or queried using our <a href="../goldenPath/help/api.html">API</a>. For more +information on accessing track data see our +<a href="../FAQ/FAQdownloads.html#download36">Track Data Access FAQ</a>. The files are associated with these tracks in the following way: <ul> <li>TransMap Ensembl - <tt>$db.ensembl.transMapV??.bigPsl</tt></li> <li>TransMap RefGene - <tt>$db.refseq.transMapV??.bigPsl</tt></li> <li>TransMap RNA - <tt>$db.rna.transMapV??.bigPsl</tt></li> <li>TransMap ESTs - <tt>$db.est.transMapV??.bigPsl</tt></li> </ul> Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range, for example: <p><tt> bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/transMap/V4/$db.refseq.transMapV4.bigPsl