4571e8f87bb083f81f671b81d7d3aef65334f2e1 markd Fri Jun 28 11:58:35 2019 -0700 made transmap download documents neutral to version diff --git src/hg/makeDb/trackDb/transMapTailer.html src/hg/makeDb/trackDb/transMapTailer.html index abe6adc..5ddcb79 100644 --- src/hg/makeDb/trackDb/transMapTailer.html +++ src/hg/makeDb/trackDb/transMapTailer.html @@ -66,37 +66,37 @@ 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/$db/transMap/V4/">download server</a>. +<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/transMap/">download server</a>. The files are associated with these tracks in the following way: <ul> -<li>TransMap Ensembl - <tt>$db.ensembl.transMapV4.bigPsl</tt></li> -<li>TransMap RefGene - <tt>$db.refseq.transMapV4.bigPsl</tt></li> -<li>TransMap RNA - <tt>$db.rna.transMapV4.bigPsl</tt></li> -<li>TransMap ESTs - <tt>$db.est.transMapV4.bigPsl</tt></li> +<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 -chrom=chr6 -start=0 -end=1000000 stdout </tt> <H2>Credits</H2> <P>