7e87cadb469b4e0eb4fb7f973154357cfe7fc345 lrnassar Mon Sep 21 15:56:18 2026 -0700 QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks. diff --git src/hg/makeDb/trackDb/human/meiEul1db.html src/hg/makeDb/trackDb/human/meiEul1db.html index e5c19ac2aff..ca3a9115d10 100644 --- src/hg/makeDb/trackDb/human/meiEul1db.html +++ src/hg/makeDb/trackDb/human/meiEul1db.html @@ -1,122 +1,123 @@ <h2>Description</h2> <p> Long Interspersed Nuclear Element-1 (LINE-1, L1) is the only retrotransposon family in modern humans that still autonomously generates new copies by an RNA-mediated copy-and-paste mechanism. The L1-HS subfamily (HS for "human-specific") is responsible for ongoing retrotransposition activity and contributes to inter-individual genetic diversity: on average, two human genomes differ at hundreds of sites with respect to L1 insertion presence or absence. New L1-HS insertions are a recognised source of germline mutation and somatic mosaicism, and have been observed in many cancers and brain tissues. </p> <p> This track shows the curated set of L1-HS insertion polymorphisms catalogued in <a href="http://eul1db.unice.fr" target="_blank">euL1db</a>, the European database of L1HS retrotransposon insertions in humans (Mir et al. 2015). Each feature is a Meta Retrotransposon Insertion Polymorphism (MRIP) — a non-redundant genomic site obtained by merging close Sample Retrotransposon Insertion Polymorphisms -(SRIPs) reported across 32 published studies covering more than 900 samples. +(SRIPs) reported across 32 published studies covering 943 samples. </p> <h2>Display Conventions and Configuration</h2> <p> Each item is a single MRIP. The score is the euL1db pseudo-allele frequency (field <i>pseudoAlleleFreq</i>) scaled to 0–1000. Items are coloured by the lineage of contributing SRIPs: </p> <p> <span style="display:inline-block; background-color:#0072B2; width:18px; height:12px; vertical-align:middle;"></span> <b>germline</b> — all contributing SRIPs are germline insertions<br> <span style="display:inline-block; background-color:#D55E00; width:18px; height:12px; vertical-align:middle;"></span> <b>somatic</b> — all contributing SRIPs are somatic insertions<br> <span style="display:inline-block; background-color:#CC79A7; width:18px; height:12px; vertical-align:middle;"></span> <b>mixed</b> — both germline and somatic SRIPs at this site<br> <span style="display:inline-block; background-color:#999999; width:18px; height:12px; vertical-align:middle;"></span> <b>unknown</b> — lineage not reported </p> <p> Clicking an item opens a detail page that lists the studies and PubMed IDs reporting the insertion, the detection methods used, the tissues, clinical conditions and populations represented, and a table of the contributing samples (truncated to 200 rows for very large aggregations — see <a href="http://eul1db.unice.fr" target="_blank">euL1db</a> for the full sample breakdown). Filters are available for pseudo-allele frequency, SRIP and study counts, lineage, PCR validation, and whether the MRIP is annotated as already present in the reference genome. </p> <h2>Methods</h2> <p> euL1db integrates published L1-HS insertion calls from a wide range of -detection assays. Most studies used enrichment-based protocols -(RC-seq, L1-seq, Ewing PCR, TIP-seq), high-throughput whole-genome -sequencing analysed with TranspoSeq, MELT or similar pipelines, or -fosmid-based long-read approaches. For each accepted study the original +detection assays. The methods behind the largest numbers of insertions are +Ewing PCR, RC-seq, Tea, L1-seq and TranspoSeq, followed by the Ewing +pipeline, Spanner, fosmid sequencing, TranspoSeq-exome and candidate-gene +assays. The detection method is recorded for every insertion and is shown +on the details page. For each accepted study the original authors' sample-level calls (SRIPs) were curated and re-mapped to hg19 where needed. SRIPs that are within 200 bp of each other on the same strand and are germline are merged into a single non-redundant MRIP. Somatic events are not merged, reflecting the unique nature of independent retrotransposition events. See Mir et al. 2015 for full curation details. </p> <p> Track files were generated from the euL1db v1.00 release (data dump downloaded March 2018, last updated 14 October 2014) using the script <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/mei/meiEul1dbToBed.py" target="_blank">meiEul1dbToBed.py</a>, which joins the MRIP, SRIP, Sample, Individual, Study and Methods tables and emits a BED9+ file. For details of the build process see the makeDoc text file -<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg19/mei.txt" - target="_blank">hg19/mei.txt</a>, and the scripts directory +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/mei.txt" + target="_blank">doc/hg38/mei.txt</a>, and the scripts directory <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/mei" - target="_blank">src/hg/makeDb/scripts/mei</a>. + target="_blank">src/hg/makeDb/scripts/mei</a>, + and the track configuration is in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/mei.ra" target="_blank">trackDb/human/mei.ra</a>. The Helman2014 study used numeric chromosome names (23 = X, 24 = Y); these were renamed in the build script. The hg19 BED was lifted to hg38 with <tt>liftOver</tt> using the standard <tt>hg19ToHg38.over.chain.gz</tt> chain. -Of 8,991 hg19 MRIPs, 8,988 lifted successfully; the 3 unlifted MRIPs are -listed in the build directory. +Of 8,991 hg19 MRIPs, 8,988 lifted successfully. </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-separated tables. From scripts, the data can be accessed through our <a href="https://api.genome.ucsc.edu" target="_blank">REST API</a>, track=<i>meiEul1db</i>. </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/hg38/mei/" target="_blank">our download +<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/mei/" target="_blank">our download server</a>. The file for this track is called <tt>eul1db.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">here</a>. +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/hg38/mei/eul1db.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt> +<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/mei/eul1db.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt> </p> <p> The original annotation source data can be downloaded from <a href="http://eul1db.unice.fr" target="_blank">eul1db.unice.fr</a> via the Download tab. </p> <h2>Credits</h2> <p> Thanks to Gaël Cristofari and colleagues at IRCAN (Nice, France) for making the euL1db data freely available, and to the original study authors whose data are aggregated. Track built at UCSC by the Genome Browser group. </p> <h2>References</h2> <p> Mir AA, Philippe C, Cristofari G. <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gku1043" target="_blank"> euL1db: the European database of L1HS retrotransposon insertions in humans</a>. <em>Nucleic Acids Res</em>. 2015 Jan;43(Database issue):D43-7. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/25352549" target="_blank">25352549</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383891/" target="_blank">PMC4383891</a> </p>