8faeb3cba60c7cb842bc17c17a57c9b53ef1b478 max Tue Apr 21 02:51:32 2026 -0700 ncbiCloneEndsCH1073: add NCBI CH1073 BAC library clone end placements track on danRer11, refs #35059 210,777 unique-concordant clone-insert placements from NCBI's CH1073 (RZPD-1073 / DanioKey) library clone report. Separate from the existing bacEndPairsLift (danRer4 -> danRer11 UCSC-BLAT lift), which is left in place. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.html src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.html new file mode 100644 index 00000000000..b18fa1a0867 --- /dev/null +++ src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.html @@ -0,0 +1,123 @@ +<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. +</p> +<p> +This track shows the NCBI <b>CH1073</b> zebrafish BAC library (also +known as RZPD-1073 / DanioKey) placements labeled by NCBI as +<i>unique concordant</i>—clones whose two end reads place +uniquely in GRCz11 and at the expected orientation and approximate +distance. Each row represents one clone insert inferred from the two +mapped ends; one clone may have several placements when the ends map +to an alt haplotype scaffold in addition to the primary assembly. +</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 that is 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. +</p> +<p> +Three categorical filters are available in the track configuration +interface: +<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 CH1073 library. 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 is +available from the NCBI FTP server at +<a href="https://ftp.ncbi.nlm.nih.gov/repository/clone/reports/Danio_rerio/" +target="_blank">ftp.ncbi.nlm.nih.gov/repository/clone/reports/Danio_rerio/</a>. +</p> +<p> +To build the UCSC track, the +<tt>CH1073.GCF_000002035.6.105.unique_concordant.gff</tt> file was +downloaded and converted to BED. RefSeq contig accessions in the GFF +(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. +A fixed <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 +BED was converted to bigBed with <tt>bedToBigBed</tt>. +</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>, <tt>track=ncbiCloneEndsCH1073</tt>. +</p> +<p> +For automated download and analysis, the annotation is stored in a +bigBed file that can be downloaded from +<a href="http://hgdownload.soe.ucsc.edu/gbdb/danRer11/ncbiCloneEndsCH1073/" +target="_blank">our download server</a>. The file for this track is +<tt>CH1073.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/ncbiCloneEndsCH1073/CH1073.bb -chrom=chr1 -start=0 -end=10000000 stdout</tt>. +</p> +<p> +The original annotation can be downloaded from +<a href="https://ftp.ncbi.nlm.nih.gov/repository/clone/reports/Danio_rerio/CH1073.GCF_000002035.6.105.unique_concordant.gff" +target="_blank">NCBI's clone reports FTP directory</a>. +</p> + +<h2>Credits</h2> +<p> +Clone placements produced by the NCBI Clone DB group. CH1073 +(RZPD-1073 / DanioKey) is a zebrafish BAC library originally +constructed and end-sequenced in the context of large-scale +zebrafish genome and clone resources. +The CH1073 library was constructed by +<a href="https://bacpacresources.org/" target="_blank">Pieter de Jong</a> +and colleagues at BACPAC Resources. +</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>