d93c426ef1ad5fbb32b754408599eaf380a199e5 max Tue Apr 21 13:34:58 2026 -0700 choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059 - Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML, makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in Methods. - Wrap the existing CH1073 track in a choriCloneEnds superTrack and add two new subtracks built from the parallel unique_concordant GFFs at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ : CH73 (99,141 placements, 23 oversize) CH211 (70,231 placements, 46 oversize) CH1073 is rebuilt with the same pipeline (210,777 placements). - Build all three bigBeds with -extraIndex=name and register searchTable / searchType bigBed stanzas with searchIndex name on each subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...) resolve from the Genome Browser position box. - Single shared HTML description page; Methods now links to the NCBI FTP source and to the UCSC makeDoc and scripts dir on GitHub. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.html src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.html new file mode 100644 index 00000000000..22770b44520 --- /dev/null +++ src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.html @@ -0,0 +1,142 @@ +<h2>Description</h2> +<p> +Bacterial artificial chromosomes (BACs) are large inserts of genomic DNA +(typically 150–300 kb) carried in bacteria. Sequencing a single +short read from each end of a BAC and mapping those end sequences to a +reference genome yields the approximate start and stop of the full BAC +insert. These BAC end placements are useful for confirming the order, +orientation, and span of the reference assembly, for identifying large +structural variants that disrupt concordant pair placement, and for +locating a BAC containing a gene of interest for downstream laboratory +work. The individual clones in all three libraries shown here can be +ordered from +<a href="https://bacpacresources.org/" target="_blank">BACPAC Resources</a> +(CHORI/BACPAC) for use at the bench. +</p> +<p> +This track container shows three CHORI (Children's Hospital Oakland +Research Institute) zebrafish BAC libraries: +<ul> +<li><b>CH1073</b> – also known as RZPD-1073 / DanioKey; 210,777 +unique-concordant placements.</li> +<li><b>CH73</b> – RZPD-73 / DanioKey Pilot; 99,141 placements.</li> +<li><b>CH211</b> – 70,231 placements.</li> +</ul> +All three libraries were end-sequenced and placed on the GRCz11 +(danRer11) assembly by the NCBI Clone DB group; only +<i>unique concordant</i> placements are shown, i.e. clones whose +two end reads place uniquely and at the expected orientation and +approximate distance. Each row represents one clone insert inferred +from a pair of mapped ends; one clone may have several placements if +its ends also map to an alt haplotype scaffold. +</p> + +<h2>Display Conventions and Configuration</h2> +<p> +Each item is drawn as a single block spanning the inferred BAC insert +(start of the upstream end to end of the downstream end). Clicking an +item opens a details page showing the clone name, NCBI placement ID, +insert size, concordance and uniqueness flags, assembly unit +(<i>Primary Assembly</i>, <i>ALT_DRER_TU_1</i>, etc.), and an +<i>oversize</i> flag set for placements larger than 500 kb +— far longer than a typical BAC — so users can filter out +likely-spurious mappings. +</p> +<p> +The clone name links out to a <a href="https://zfin.org/search" +target="_blank">ZFIN</a> search for cross-reference information on the +clone. Clone names (e.g. <tt>CH1073-100A1</tt>, <tt>CH73-1A1</tt>, +<tt>CH211-1A1</tt>) are indexed and can be entered directly in the +Genome Browser position/search box to jump to a clone. +</p> +<p> +Three categorical filters are available in each subtrack: +<ul> + <li><b>End-pair concordance</b> – <tt>TRUE</tt>/<tt>FALSE</tt></li> + <li><b>Unique placement</b> – <tt>TRUE</tt>/<tt>FALSE</tt></li> + <li><b>Oversize placement (>500kb)</b> – <tt>TRUE</tt>/<tt>FALSE</tt></li> +</ul> +By default no filter is applied. +</p> + +<h2>Methods</h2> +<p> +The source data were produced by the NCBI Clone DB group from end +sequences of the three CHORI libraries. NCBI maps each end sequence to +the reference assembly and categorizes the pair as concordant (expected +orientation and insert size) or discordant, and as uniquely placed or +multiply placed. The full set of per-library placement reports for +zebrafish is available from the NCBI FTP server at +<a href="https://ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/" +target="_blank">ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/</a>. +</p> +<p> +To build the UCSC tracks, the three +<tt>*.GCF_000002035.6.105.unique_concordant.gff</tt> files were +downloaded and converted to BED. RefSeq contig accessions in the GFFs +(e.g. <tt>NC_007114.7</tt>, <tt>NW_018394540.1</tt>) were mapped to +UCSC-style chromosome names (e.g. <tt>chr3</tt>, +<tt>chr1_KZ114997v1_alt</tt>) using the NCBI GRCz11 assembly report. +An <i>oversize</i> flag was set on any insert longer than 500 kb; +these records are retained so researchers can inspect them but are +easy to exclude via the track filter. The resulting BEDs were converted +to bigBed with <tt>bedToBigBed</tt> using a <tt>name</tt> search index +so clone names can be looked up from the browser position box. +</p> +<p> +The step-by-step track build commands (downloads, RefSeq-to-UCSC +mapping, BED conversion, bigBed build) are recorded in the UCSC +makeDoc for this track: +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/danRer11/choriCloneEnds.txt" +target="_blank">src/hg/makeDb/doc/danRer11/choriCloneEnds.txt</a>. +The GFF-to-BED converter, the RefSeq-to-UCSC mapping script, and the +autoSql schema live in +<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/choriCloneEnds" +target="_blank">src/hg/makeDb/scripts/choriCloneEnds/</a>. +</p> + +<h2>Data Access</h2> +<p> +The data can be explored interactively in table format with the +<a href="../cgi-bin/hgTables">Table Browser</a> or the +<a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported +from there to spreadsheet or tab-sep tables. From scripts, the data +can be accessed through our <a href="https://api.genome.ucsc.edu" +target="_blank">API</a>, with +<tt>track=choriCloneEndsCH1073</tt>, +<tt>track=choriCloneEndsCH73</tt>, or +<tt>track=choriCloneEndsCH211</tt>. +</p> +<p> +For automated download and analysis, each library's annotation is +stored in a bigBed file that can be downloaded from +<a href="http://hgdownload.soe.ucsc.edu/gbdb/danRer11/choriCloneEnds/" +target="_blank">our download server</a>: <tt>CH1073.bb</tt>, +<tt>CH73.bb</tt>, <tt>CH211.bb</tt>. 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" +target="_blank">here</a>. The tool can also be used to obtain features +within a given range, e.g. +<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer11/choriCloneEnds/CH1073.bb -chrom=chr1 -start=0 -end=10000000 stdout</tt>. +</p> + +<h2>Credits</h2> +<p> +Clone placements produced by the NCBI Clone DB group. The CHORI +zebrafish BAC libraries (CH73, CH211, CH1073) were constructed by +<a href="https://bacpacresources.org/" target="_blank">Pieter de Jong</a> +and colleagues at BACPAC Resources (CHORI/BACPAC). +</p> + +<h2>References</h2> +<p> +Schneider VA, Chen HC, Clausen C, Meric PA, Zhou Z, Bouk N, Husain N, Maglott DR, Church DM. +<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gks1164" target="_blank"> +Clone DB: an integrated NCBI resource for clone-associated data</a>. +<em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D1070-8. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23193260" target="_blank">23193260</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531087/" target="_blank">PMC3531087</a> +</p>