156d289f517d82c4d5a8c59981dfec21a715af8d lrnassar Mon Sep 21 09:22:45 2026 -0700 Fiber-seq QA fixes: take sample class from the lab's own table, pin the overlay draw order, and correct the description pages. refs #36210 Sample class had been guessed from the free-text cell type with a two-name exception list, which filed five lymphoblastoid lines as HPRC that are not. It now comes from a fifth column in fiberSeqSamples.tsv carrying the classification the lab supplies, and sampleClass()/NOT_HPRC are gone. Facet counts go from 25/16 to 20/21. The CpG difference track is a solidOverlay whose four files hold the same value at a shared base, so the tier drawn last is the colour the reader sees. Its children inherited a single priority from the parent, trackPriCmp ties on that, and slSort is not stable, so the paint order was arbitrary and p<0.01 was covering p<0.0001. The four levels and the two haplotype children now carry explicit priorities. At chr20:29,300,000-29,305,000 red goes from 2 image columns to 88. CpG haplotype children take their shortLabel prefix from their container, so they read "<sample> CpG Hap1" rather than colliding with the accessibility children's "<sample> Hap1". 82 labels were duplicated. Description pages: fiberSeqAcc.html attached the FIRE score's "fewer than four elements" cutoff to the percent accessible signal, which is a different quantity; two pages overstated how many of the lymphoblastoid lines come from HPRC; both pages told readers to query the API with container track names, which it refuses by design. Also documents GM12878's trio phasing and the FDR ceiling at 100, corrects the difference track's stated range, replaces a non-ASCII author name with numeric entities, and adds db= to hgTrackUi links. makeDoc: corrects a basesCovered figure that was out by a factor of a hundred, refreshes the peak file sizes after the PM00001 reissue, rewrites the sampleClass rationale, and records why multiWig children need their own priority. diff --git src/hg/makeDb/scripts/fiberSeq/fiberSeqSamples.tsv src/hg/makeDb/scripts/fiberSeq/fiberSeqSamples.tsv index cbb244e64ec..42ad73e7ccb 100644 --- src/hg/makeDb/scripts/fiberSeq/fiberSeqSamples.tsv +++ src/hg/makeDb/scripts/fiberSeq/fiberSeqSamples.tsv @@ -1,42 +1,42 @@ -#accession sample cellType hash -PM00001 GM12878 Lymphoblastoid B-lymphocyte EBV-transformed 56c8efa47d30e7ffa5b12ebe6dd1e7c4 -PM00002 HG002 Lymphoblastoid B-lymphocyte EBV-transformed 66537188deac5f1b93fbaeb25bc42e01 -PM00004 K562 Erythroleukemia myeloid bab7c68a9ebb7a2b3c7201c7a7f4c2bf -PM00005 HepG2 Hepatocyte liver 2917f9bdc4cdf28720fa5bf81eafb876 -PM00006 Panc1 Pancreatic ductal epithelial d73722295e681ecf85cd2e65aa0e7c70 -PM00007 THP-1 Monocyte myeloid d9bace2630b732dea835e6faa6a357da -PM00008 Hap1 Myeloid near-haploid 09ce0ae0ea79bd7a84b97ddc9a32fb38 -PM00009 Jurkat T-lymphocyte 41ffee46fb1292f6566d022e01d256c1 -PM00010 H1 Embryonic stem cell c8a8d41383128a1e3d26c4e5ff6754aa -PM00011 H9 Embryonic stem cell 919ef478b700e2788cfb45d787ef0e96 -PM00012 Hek293T Human embryonic kidney eb6e7dc0f85e205f584c65645f6da4b3 -PS00971 HG01123 Lymphoblastoid B-lymphocyte EBV-transformed 32075e85354ac89edd4e9472caa93d3c -PS00972 HG01258 Lymphoblastoid B-lymphocyte EBV-transformed 6131088532f16569cdfadb303c9251ff -PS00973 HG01358 Lymphoblastoid B-lymphocyte EBV-transformed 868b57a6e0470f9b749761dc80c1d4b4 -PS00974 HG01361 Lymphoblastoid B-lymphocyte EBV-transformed 89b91e72dd977f456b2a00eb548d8c76 -PS00975 HG01891 Lymphoblastoid B-lymphocyte EBV-transformed 5497a65db4b1dc18f78e0fde852ca084 -PS00976 HG02071 Lymphoblastoid B-lymphocyte EBV-transformed 29ea847693b3d38d0d2849603df73cb2 -PS00977 HG02074 Lymphoblastoid B-lymphocyte EBV-transformed dca57606102ce19dc9a99d788a2a3171 -PS00978 HG02132 Lymphoblastoid B-lymphocyte EBV-transformed 8ccfe29ff5a0093e8cfad2a727054d97 -PS00979 HG02135 Lymphoblastoid B-lymphocyte EBV-transformed fa42dfae0df70d9bce4389a1b4681238 -PS00980 HG02257 Lymphoblastoid B-lymphocyte EBV-transformed a340d9c3be89ac455752fb407495d6e3 -PS00981 HG02486 Lymphoblastoid B-lymphocyte EBV-transformed e148a02e55a49027536fa02cf1ad054b -PS00982 HG02559 Lymphoblastoid B-lymphocyte EBV-transformed 885268787c41c09ed7c1cabe8c1e6fc1 -PS00983 HG02572 Lymphoblastoid B-lymphocyte EBV-transformed e5e3af18c23d821a70086aec8262fdc8 -PS00984 HG02717 Lymphoblastoid B-lymphocyte EBV-transformed 49dd2cf0726a10a4d8eb2c8221b6f8ac -PS00985 HG02886 Lymphoblastoid B-lymphocyte EBV-transformed a352ed22ad490f183e1a89fc600c55dc -PS00986 HG03516 Lymphoblastoid B-lymphocyte EBV-transformed e9150edc165f21c8b60f524e32232b34 -PS00987 HG03804 Lymphoblastoid B-lymphocyte EBV-transformed 9bcdcdbfedc59d7fef2cae0f1acbe3ea -PS00988 HG03942 Lymphoblastoid B-lymphocyte EBV-transformed 67b785f2ac06480aff5811f5f668d6b4 -PS00989 HG04160 Lymphoblastoid B-lymphocyte EBV-transformed c29fefa1065e2cc26d914d6c79891535 -PS00990 HG04187 Lymphoblastoid B-lymphocyte EBV-transformed 98c0504758e3c8cf4383f22658aac113 -PS01302 A549 Lung epithelial adenocarcinoma 7b39ec1b123ae87b077dafc7d9090a1c -PS01305 MCF-7 Breast epithelial adenocarcinoma 3f29e4e4b63b744ce4aeb72bbeecd70f -PS01314 HCT116 Colon epithelial colorectal carcinoma 91cbfbadf9e012ed9a83a8987f7d12dd -PS01319 Caco-2 Colon epithelial colorectal adenocarcinoma c26fd5d56fd09f84ff28c7c4b9f99559 -PS01388 WTC-11 Induced pluripotent stem cell iPSC 85dce624f9c36c4f2ff11bc22af93dd1 -PS01517 GM28572 Lymphoblastoid B-lymphocyte EBV-transformed 0b5ee552d04d5730df674bd9ab288ce9 -PS01518 GM28570 Lymphoblastoid B-lymphocyte EBV-transformed f185df42c50391eebc7e3b69d5fd945f -PS01519 GM25456 Lymphoblastoid B-lymphocyte EBV-transformed 5612ea912092183984914c6d25998b1f -PS01520 GM25455 Lymphoblastoid B-lymphocyte EBV-transformed 27d0455403f6b4221c7267604c468aff -PS01524 GM27730 Lymphoblastoid B-lymphocyte EBV-transformed 8f7783e80526113d9dda6bb3ed387bee +#accession sample cellType hash sampleClass +PM00001 GM12878 Lymphoblastoid B-lymphocyte EBV-transformed 56c8efa47d30e7ffa5b12ebe6dd1e7c4 Common Cell Line +PM00002 HG002 Lymphoblastoid B-lymphocyte EBV-transformed 66537188deac5f1b93fbaeb25bc42e01 Common Cell Line +PM00004 K562 Erythroleukemia myeloid bab7c68a9ebb7a2b3c7201c7a7f4c2bf Common Cell Line +PM00005 HepG2 Hepatocyte liver 2917f9bdc4cdf28720fa5bf81eafb876 Common Cell Line +PM00006 Panc1 Pancreatic ductal epithelial d73722295e681ecf85cd2e65aa0e7c70 Common Cell Line +PM00007 THP-1 Monocyte myeloid d9bace2630b732dea835e6faa6a357da Common Cell Line +PM00008 Hap1 Myeloid near-haploid 09ce0ae0ea79bd7a84b97ddc9a32fb38 Common Cell Line +PM00009 Jurkat T-lymphocyte 41ffee46fb1292f6566d022e01d256c1 Common Cell Line +PM00010 H1 Embryonic stem cell c8a8d41383128a1e3d26c4e5ff6754aa Common Cell Line +PM00011 H9 Embryonic stem cell 919ef478b700e2788cfb45d787ef0e96 Common Cell Line +PM00012 Hek293T Human embryonic kidney eb6e7dc0f85e205f584c65645f6da4b3 Common Cell Line +PS00971 HG01123 Lymphoblastoid B-lymphocyte EBV-transformed 32075e85354ac89edd4e9472caa93d3c HPRC +PS00972 HG01258 Lymphoblastoid B-lymphocyte EBV-transformed 6131088532f16569cdfadb303c9251ff HPRC +PS00973 HG01358 Lymphoblastoid B-lymphocyte EBV-transformed 868b57a6e0470f9b749761dc80c1d4b4 HPRC +PS00974 HG01361 Lymphoblastoid B-lymphocyte EBV-transformed 89b91e72dd977f456b2a00eb548d8c76 HPRC +PS00975 HG01891 Lymphoblastoid B-lymphocyte EBV-transformed 5497a65db4b1dc18f78e0fde852ca084 HPRC +PS00976 HG02071 Lymphoblastoid B-lymphocyte EBV-transformed 29ea847693b3d38d0d2849603df73cb2 HPRC +PS00977 HG02074 Lymphoblastoid B-lymphocyte EBV-transformed dca57606102ce19dc9a99d788a2a3171 HPRC +PS00978 HG02132 Lymphoblastoid B-lymphocyte EBV-transformed 8ccfe29ff5a0093e8cfad2a727054d97 HPRC +PS00979 HG02135 Lymphoblastoid B-lymphocyte EBV-transformed fa42dfae0df70d9bce4389a1b4681238 HPRC +PS00980 HG02257 Lymphoblastoid B-lymphocyte EBV-transformed a340d9c3be89ac455752fb407495d6e3 HPRC +PS00981 HG02486 Lymphoblastoid B-lymphocyte EBV-transformed e148a02e55a49027536fa02cf1ad054b HPRC +PS00982 HG02559 Lymphoblastoid B-lymphocyte EBV-transformed 885268787c41c09ed7c1cabe8c1e6fc1 HPRC +PS00983 HG02572 Lymphoblastoid B-lymphocyte EBV-transformed e5e3af18c23d821a70086aec8262fdc8 HPRC +PS00984 HG02717 Lymphoblastoid B-lymphocyte EBV-transformed 49dd2cf0726a10a4d8eb2c8221b6f8ac HPRC +PS00985 HG02886 Lymphoblastoid B-lymphocyte EBV-transformed a352ed22ad490f183e1a89fc600c55dc HPRC +PS00986 HG03516 Lymphoblastoid B-lymphocyte EBV-transformed e9150edc165f21c8b60f524e32232b34 HPRC +PS00987 HG03804 Lymphoblastoid B-lymphocyte EBV-transformed 9bcdcdbfedc59d7fef2cae0f1acbe3ea HPRC +PS00988 HG03942 Lymphoblastoid B-lymphocyte EBV-transformed 67b785f2ac06480aff5811f5f668d6b4 HPRC +PS00989 HG04160 Lymphoblastoid B-lymphocyte EBV-transformed c29fefa1065e2cc26d914d6c79891535 HPRC +PS00990 HG04187 Lymphoblastoid B-lymphocyte EBV-transformed 98c0504758e3c8cf4383f22658aac113 HPRC +PS01302 A549 Lung epithelial adenocarcinoma 7b39ec1b123ae87b077dafc7d9090a1c Common Cell Line +PS01305 MCF-7 Breast epithelial adenocarcinoma 3f29e4e4b63b744ce4aeb72bbeecd70f Common Cell Line +PS01314 HCT116 Colon epithelial colorectal carcinoma 91cbfbadf9e012ed9a83a8987f7d12dd Common Cell Line +PS01319 Caco-2 Colon epithelial colorectal adenocarcinoma c26fd5d56fd09f84ff28c7c4b9f99559 Common Cell Line +PS01388 WTC-11 Induced pluripotent stem cell iPSC 85dce624f9c36c4f2ff11bc22af93dd1 Common Cell Line +PS01517 GM28572 Lymphoblastoid B-lymphocyte EBV-transformed 0b5ee552d04d5730df674bd9ab288ce9 Common Cell Line +PS01518 GM28570 Lymphoblastoid B-lymphocyte EBV-transformed f185df42c50391eebc7e3b69d5fd945f Common Cell Line +PS01519 GM25456 Lymphoblastoid B-lymphocyte EBV-transformed 5612ea912092183984914c6d25998b1f Common Cell Line +PS01520 GM25455 Lymphoblastoid B-lymphocyte EBV-transformed 27d0455403f6b4221c7267604c468aff Common Cell Line +PS01524 GM27730 Lymphoblastoid B-lymphocyte EBV-transformed 8f7783e80526113d9dda6bb3ed387bee Common Cell Line