4f8f8773bec66a9e993e9897e0b032c6e97dead8 max Fri May 15 10:12:29 2026 -0700 mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524 diff --git src/hg/makeDb/trackDb/human/meiEul1dbRef.html src/hg/makeDb/trackDb/human/meiEul1dbRef.html new file mode 100644 index 00000000000..af70e9a4b85 --- /dev/null +++ src/hg/makeDb/trackDb/human/meiEul1dbRef.html @@ -0,0 +1,94 @@ +<h2>Description</h2> +<p> +This track shows the L1-HS (human-specific LINE-1) retrotransposon copies that are +already present in the human reference genome, as catalogued by +<a href="http://eul1db.unice.fr" target="_blank">euL1db</a>. Unlike the companion +<a href="hgTrackUi?g=meiEul1db">euL1db Insertions</a> track, which shows polymorphic +insertions not present (or variably present) in the reference, the items here are +the L1-HS copies that the reference genome already contains. Together, the two +tracks provide a comprehensive view of L1-HS positions in the genome — both +the "fixed" reference set and the variants segregating in the human +population. +</p> + +<h2>Display Conventions and Configuration</h2> +<p> +Each item is a single reference L1-HS element. The name shows the L1HS sub-group. +Items are coloured by sub-group: +</p> +<p> +<span style="display:inline-block; background-color:#0072B2; width:18px; height:12px; vertical-align:middle;"></span> +<b>L1HS-Ta</b> — youngest, currently active L1-HS subset<br> +<span style="display:inline-block; background-color:#E69F00; width:18px; height:12px; vertical-align:middle;"></span> +<b>L1HS-PreTa</b> — older L1-HS subset, ancestral to Ta<br> +<span style="display:inline-block; background-color:#999999; width:18px; height:12px; vertical-align:middle;"></span> +<b>L1HS-undef</b> — sub-group not assigned in euL1db +</p> +<p> +The detail page for each element shows the element length, its integrity +(full-length, 5′-truncated, 3′-truncated, internal_fragment), and its +position on the L1HS consensus sequence. Filters are provided for sub-group and +integrity. +</p> + +<h2>Methods</h2> +<p> +The reference L1-HS catalogue was assembled by the euL1db curators by aligning +the L1HS consensus sequence to the hg19 reference genome and classifying each +match into one of the L1HS sub-groups. See Mir et al. 2015 for further details. +</p> +<p> +Track files were generated from the euL1db v1.00 ReferenceL1HS.txt table (data +dump downloaded March 2018) using the script +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/mei/meiEul1dbRefToBed.py" + target="_blank">meiEul1dbRefToBed.py</a>. The hg19 BED was lifted to hg38 with +<tt>liftOver</tt>; of 1,544 hg19 elements, 1,540 lifted successfully. For +details see +<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/tree/master/src/hg/makeDb/scripts/mei" + target="_blank">src/hg/makeDb/scripts/mei</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-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>meiEul1dbRef</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 +server</a>. The file for this track is called <tt>eul1dbRef.bb</tt>. Individual +regions or the whole genome annotation can be obtained using our tool +<tt>bigBedToBed</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. 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> +