docs: update examples to use hg38 as primary reference genome#1046
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etal merged 2 commits intoetal:masterfrom Apr 15, 2026
Merged
docs: update examples to use hg38 as primary reference genome#1046etal merged 2 commits intoetal:masterfrom
etal merged 2 commits intoetal:masterfrom
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hg38 does not have an encodeDCC/wgEncodeMapability directory on UCSC. Point to the hg38 bigZips directory for current data, and keep the hg19 ENCODE link for legacy workflows.
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Summary
Update documentation to use hg38/GRCh38 as the primary reference genome in all examples, while preserving hg19 references for legacy workflows.
Background
PR #837 added hg38 data files (
data/refFlat_hg38.txt,data/access-10kb.hg38.bed) but the documentation still defaulted to hg19 examples. hg38 has been the standard reference for over 10 years.Changes
doc/pipeline.rstdoc/quickstart.rstdoc/nonhybrid.rstdoc/scripts.rstKey decisions
data/access-10kb.hg38.bedanddata/refFlat_hg38.txt(both already exist in repo)data/for legacy workflows"encodeDCC/wgEncodeMapability/— points tobigZips/instead, with hg19 fallback linkRef #822