7713a08da69691ba499d5b9d44379c43e8cdb608 markd Fri Sep 18 09:27:52 2026 -0700 Adding Transcription Start container with ENCODE 4 PRO-cap and ProCapNet tracks. refs #35528 New superTrack transcriptionStart in the rna group, holding two faceted composites: encode4ProCap with PRO-cap measurements and proCapNet with the model predictions and sequence-contribution scores. hg38 has all three data types, hs1 the predictions only. ENCODE 4 PRO-cap comes from the portal rather than the submitter's hub copy. For each of the six experiments only the plus and minus strand signal of unique reads files of that experiment's default analysis are taken, which drops files superseded by a later reprocessing. ENCODE publishes no pooled file, so the per-replicate files are summed per cell line and strand, the same merge the ProCapNet models were trained on. Total signal is conserved exactly. The published ProCapNet prediction bigWigs store one bedGraph interval per base and hold a literal NaN at every unresolved (N) base on hg38, which makes autoScale and every summary statistic NaN. They are re-encoded into fixedStep sections, a third smaller with no value changed, dropping 164,268,582 NaN bases of 3,088,269,832 on hg38 and none on hs1. Losslessness verified against the originals on random windows across five chromosomes. The composites are faceted rather than plain because a container multiWig under a plain composite is flattened away by hgTrackUi and never drawn. Each cell line is one row with a checkbox per data type, a Sample class facet, ENCODE accession links and a Files column linking each bigWig on hgdownload. Scripts and the cell line configuration are in makeDb/outside/proCapNet; the trackDb stanzas and the faceted metadata tables are generated, not hand edited. Claude-Session: https://claude.ai/code/session_01LAB6jWshLvB7eNXQKWVuW5 diff --git src/hg/makeDb/outside/proCapNet/proCapNetExperiments.tsv src/hg/makeDb/outside/proCapNet/proCapNetExperiments.tsv new file mode 100644 index 00000000000..8c2f7221833 --- /dev/null +++ src/hg/makeDb/outside/proCapNet/proCapNetExperiments.tsv @@ -0,0 +1,7 @@ +cell hubCell tissue sampleClass procapAcc modelAcc color +A673 A673 Muscle Cancer ENCSR046BCI ENCSR072YCM 0,114,178 +Caco-2 CACO2 Colon Cancer ENCSR100LIJ ENCSR182QNJ 213,94,0 +Calu3 CALU3 Lung Cancer ENCSR935RNW ENCSR797DEF 0,158,115 +HUVEC HUVEC Blood vessel Non-cancer ENCSR098LLB ENCSR801ECP 204,121,167 +K562 K562 Blood Cancer ENCSR261KBX ENCSR740IPL 230,159,0 +MCF10A MCF10A Breast Non-cancer ENCSR799DGV ENCSR860TYZ 86,180,233