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/doc/hg19.txt src/hg/makeDb/doc/hg19.txt index e3c5eef2820..03b1ce75338 100644 --- src/hg/makeDb/doc/hg19.txt +++ src/hg/makeDb/doc/hg19.txt @@ -36083,15 +36083,31 @@ # build/hg19/tadsSchmitt<code>.bb (21 files; native hg19, no liftOver). ############################################################################## # McArthur 2021 TAD boundary stability (tadsMcArthur) - NATIVE hg19 (no lift) ############################################################################## # GitHub emcarthur/TAD-stability-heritability, 100kbBookendBoundaries_byStability.bed (hg19, # 14,345 boundaries, 100 kb; cols chr loc loc2 counts percentile). Drop header, bedToBigBed # -type=bed5+2 -as=tadStability.as -> build/hg19/tadsMcArthur.bb (14,344). bed5+2: name, # score=round(contexts/37*1000) (render proxy), contexts (1-37), percentile. # gbdb: /gbdb/hg19/bbi/tad/{tadsDixon*,tadsSchmitt*,tadsMcArthur}.bb (symlinks to build/hg19/). # trackDb: human/hg19/tad.ra (priorities Dixon 1 / Schmitt 2 / McArthur 3; superTrack on hide; # Dixon visibility pack, Schmitt+McArthur hide) + tads/tadsDixon/tadsSchmitt/tadsMcArthur .html. # Gated: include tad.ra alpha in human/hg19/trackDb.ra. cd ~/kent/src/hg/makeDb/trackDb && make DBS=hg19 FIND=find + +######################################################################### +# mei - Mobile Element Insertions, euL1db subtracks (DONE 2026-09-21 Lou) +# refs #37524 +# +# hg19 carries two of the six subtracks of the "Mobile Insertions" (mei) +# superTrack: meiEul1db (8,991 curated L1-HS insertion polymorphisms) and +# meiEul1dbRef (1,544 reference-genome L1HS copies), both from euL1db +# v1.00 (Mir et al. 2015, PMID 25352549). euL1db's coordinates are hg19 +# natively; the hg38 copies are lifted from these. +# +# The stanza lives in trackDb/human/mei.ra (shared across assemblies via +# $D) and every build step for both assemblies is documented together in: +# ~/kent/src/hg/makeDb/doc/hg38/mei.txt +# +# Files: /gbdb/hg19/mei/eul1db.bb, /gbdb/hg19/mei/eul1dbRef.bb