acf20930c5cdfa1e352826a702ad8f36344178c4 markd Thu Sep 24 21:16:13 2026 -0700 Fixes from an independent review of the TSS tracks. refs #35528 The Data Access sections told users to pass the composite name to the API, which returns HTTP 400. The API serves one bigWig at a time, so both pages now name a single strand of one cell line, verified to return 200. encode4ProCap.html claimed the kent tree held the manifest of which ENCODE files went into each track, and it did not. Commit that manifest as proCapNetEncodeFiles.tsv and name it on the page. It matters because proCapNetEncodeMeta resolves each experiment's default analysis at run time, so re-running it after an ENCODE reprocessing can pick different files. Cite Shah et al. for the ENCODE 4 nascent transcriptome survey the six PRO-cap experiments come from. Sagar Shah was credited by name with no reference. The hg38 makedoc called the 164268582 dropped bases "the N regions", but gap on the primary chromosomes is 150610728. The extra 13.7 Mb is sequence flanking each gap, dropped because most of its 2114 bp window was unresolved. diff --git src/hg/makeDb/outside/proCapNet/proCapNetEncodeFiles.tsv src/hg/makeDb/outside/proCapNet/proCapNetEncodeFiles.tsv new file mode 100644 index 00000000000..3714a8a9155 --- /dev/null +++ src/hg/makeDb/outside/proCapNet/proCapNetEncodeFiles.tsv @@ -0,0 +1,27 @@ +cell encodeAcc analysisAcc fileAcc strand bioRep techRep size url +A673 ENCSR046BCI ENCAN728WTG ENCFF771KSZ pos 2 2_1 12516653 https://www.encodeproject.org/files/ENCFF771KSZ/@@download/ENCFF771KSZ.bigWig +A673 ENCSR046BCI ENCAN728WTG ENCFF862PQN neg 2 2_1 12405434 https://www.encodeproject.org/files/ENCFF862PQN/@@download/ENCFF862PQN.bigWig +A673 ENCSR046BCI ENCAN728WTG ENCFF418SHY pos 1 1_1 18711710 https://www.encodeproject.org/files/ENCFF418SHY/@@download/ENCFF418SHY.bigWig +A673 ENCSR046BCI ENCAN728WTG ENCFF280DDJ neg 1 1_1 18531846 https://www.encodeproject.org/files/ENCFF280DDJ/@@download/ENCFF280DDJ.bigWig +Caco-2 ENCSR100LIJ ENCAN949HJF ENCFF790ZZN pos 2 2_1 16186005 https://www.encodeproject.org/files/ENCFF790ZZN/@@download/ENCFF790ZZN.bigWig +Caco-2 ENCSR100LIJ ENCAN949HJF ENCFF320FTM pos 1 1_1 14057310 https://www.encodeproject.org/files/ENCFF320FTM/@@download/ENCFF320FTM.bigWig +Caco-2 ENCSR100LIJ ENCAN949HJF ENCFF174MJP neg 2 2_1 16034179 https://www.encodeproject.org/files/ENCFF174MJP/@@download/ENCFF174MJP.bigWig +Caco-2 ENCSR100LIJ ENCAN949HJF ENCFF635VJZ neg 1 1_1 16926132 https://www.encodeproject.org/files/ENCFF635VJZ/@@download/ENCFF635VJZ.bigWig +Calu3 ENCSR935RNW ENCAN268XGN ENCFF199SAQ neg 2 2_1 22148424 https://www.encodeproject.org/files/ENCFF199SAQ/@@download/ENCFF199SAQ.bigWig +Calu3 ENCSR935RNW ENCAN268XGN ENCFF057WPU pos 1 1_1 14442589 https://www.encodeproject.org/files/ENCFF057WPU/@@download/ENCFF057WPU.bigWig +Calu3 ENCSR935RNW ENCAN268XGN ENCFF979DPW neg 1 1_1 14338061 https://www.encodeproject.org/files/ENCFF979DPW/@@download/ENCFF979DPW.bigWig +Calu3 ENCSR935RNW ENCAN268XGN ENCFF107MGL pos 2 2_1 18400730 https://www.encodeproject.org/files/ENCFF107MGL/@@download/ENCFF107MGL.bigWig +HUVEC ENCSR098LLB ENCAN503GAY ENCFF807QNT neg 1 1_1 25826766 https://www.encodeproject.org/files/ENCFF807QNT/@@download/ENCFF807QNT.bigWig +HUVEC ENCSR098LLB ENCAN503GAY ENCFF261GXH pos 1 1_1 26029712 https://www.encodeproject.org/files/ENCFF261GXH/@@download/ENCFF261GXH.bigWig +K562 ENCSR261KBX ENCAN284RAQ ENCFF580QEK pos 2 2_1 17002019 https://www.encodeproject.org/files/ENCFF580QEK/@@download/ENCFF580QEK.bigWig +K562 ENCSR261KBX ENCAN284RAQ ENCFF253HUA neg 1 1_1 7198572 https://www.encodeproject.org/files/ENCFF253HUA/@@download/ENCFF253HUA.bigWig +K562 ENCSR261KBX ENCAN284RAQ ENCFF328OOU neg 2 2_1 16835156 https://www.encodeproject.org/files/ENCFF328OOU/@@download/ENCFF328OOU.bigWig +K562 ENCSR261KBX ENCAN284RAQ ENCFF994CSC pos 1 1_1 7353114 https://www.encodeproject.org/files/ENCFF994CSC/@@download/ENCFF994CSC.bigWig +MCF10A ENCSR799DGV ENCAN003PYP ENCFF952WWA pos 2 2_1 13978459 https://www.encodeproject.org/files/ENCFF952WWA/@@download/ENCFF952WWA.bigWig +MCF10A ENCSR799DGV ENCAN003PYP ENCFF221GWZ pos 1 1_1 23631443 https://www.encodeproject.org/files/ENCFF221GWZ/@@download/ENCFF221GWZ.bigWig +MCF10A ENCSR799DGV ENCAN003PYP ENCFF227BQW neg 1 1_1 13254847 https://www.encodeproject.org/files/ENCFF227BQW/@@download/ENCFF227BQW.bigWig +MCF10A ENCSR799DGV ENCAN003PYP ENCFF572ZPQ pos 2 2_1 16585030 https://www.encodeproject.org/files/ENCFF572ZPQ/@@download/ENCFF572ZPQ.bigWig +MCF10A ENCSR799DGV ENCAN003PYP ENCFF074ZFW neg 2 2_1 19934994 https://www.encodeproject.org/files/ENCFF074ZFW/@@download/ENCFF074ZFW.bigWig +MCF10A ENCSR799DGV ENCAN003PYP ENCFF114DBY neg 2 2_1 13852316 https://www.encodeproject.org/files/ENCFF114DBY/@@download/ENCFF114DBY.bigWig +MCF10A ENCSR799DGV ENCAN003PYP ENCFF566EAN pos 1 1_1 13341092 https://www.encodeproject.org/files/ENCFF566EAN/@@download/ENCFF566EAN.bigWig +MCF10A ENCSR799DGV ENCAN003PYP ENCFF704RON neg 1 1_1 23397271 https://www.encodeproject.org/files/ENCFF704RON/@@download/ENCFF704RON.bigWig