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) diff --git src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.html src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.html deleted file mode 100644 index b18fa1a0867..00000000000 --- src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.html +++ /dev/null @@ -1,123 +0,0 @@ -

Description

-

-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. -

-

-This track shows the NCBI CH1073 zebrafish BAC library (also -known as RZPD-1073 / DanioKey) placements labeled by NCBI as -unique concordant—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. -

- -

Display Conventions and Configuration

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-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 -(Primary Assembly, ALT_DRER_TU_1, etc.), and an -oversize flag that is set for placements larger than -500 kb—far longer than a typical BAC—so users can -filter out likely-spurious mappings. -

-

-The clone name links out to a ZFIN search for cross-reference information on the -clone. -

-

-Three categorical filters are available in the track configuration -interface: -

-By default no filter is applied. -

- -

Methods

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-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 -ftp.ncbi.nlm.nih.gov/repository/clone/reports/Danio_rerio/. -

-

-To build the UCSC track, the -CH1073.GCF_000002035.6.105.unique_concordant.gff file was -downloaded and converted to BED. RefSeq contig accessions in the GFF -(e.g. NC_007114.7, NW_018394540.1) were mapped to -UCSC-style chromosome names (e.g. chr3, -chr1_KZ114997v1_alt) using the NCBI GRCz11 assembly report. -A fixed oversize 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 bedToBigBed. -

- -

Data Access

-

-The data can be explored interactively in table format with the -Table Browser or the -Data Integrator and exported -from there to spreadsheet or tab-sep tables. From scripts, the data -can be accessed through our API, track=ncbiCloneEndsCH1073. -

-

-For automated download and analysis, the annotation is stored in a -bigBed file that can be downloaded from -our download server. The file for this track is -CH1073.bb. Individual regions or the whole genome annotation -can be obtained using our tool bigBedToBed, 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 -here. The tool can also be used to obtain features -within a given range, e.g. -bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer11/ncbiCloneEndsCH1073/CH1073.bb -chrom=chr1 -start=0 -end=10000000 stdout. -

-

-The original annotation can be downloaded from -NCBI's clone reports FTP directory. -

- -

Credits

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-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 -Pieter de Jong -and colleagues at BACPAC Resources. -

- -

References

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-Schneider VA, Chen HC, Clausen C, Meric PA, Zhou Z, Bouk N, Husain N, Maglott DR, Church DM. - -Clone DB: an integrated NCBI resource for clone-associated data. -Nucleic Acids Res. 2013 Jan;41(Database issue):D1070-8. -PMID: 23193260; PMC: PMC3531087 -