Repository navigation
feat: add hs1_chrR as a supported reference genome #117
Description
Summary
Add support for the hs1_chrR reference genome in ASPEN. This is a variant of the
existing hs1 (T2T CHM13v2.0) reference but restricted to canonical chromosomes only
(chrR = "chromosomes only" subset, no alt/patch/unplaced contigs). Requested by
@wuy24 for project CCRTEGS6.
Background
hs1 is already supported. hs1_chrR follows the same pattern as other _chrR-style
references and requires the same set of resource files to be built/registered.
Tasks
1. Bowtie2 index + accessory index files (Biowulf /data/CCBR_Pipeliner/db/PipeDB/Indices/)
Build or locate the existing index directory and verify the following files exist:
-
hs1_chrR/indexes/hs1_chrR.fa— genome FASTA -
hs1_chrR/indexes/hs1_chrR.genome— chrom sizes (required by MACS2) -
hs1_chrR/indexes/*.bt2l— Bowtie2 index files (large index format, genome > 4 GB) -
hs1_chrR/indexes/hs1_chrR.Ns.bed.gz— N-regions bed (optional, used by Genrich-E) -
hs1_chrR/indexes/hs1_chrR.blacklist.bed.gz— blacklist BED (optional, used by Genrich-E)
2. Pipeline resource files (under resources/)
Create and add the following files (follow the hs1 equivalents as templates):
-
resources/chroms/hs1_chrR.chroms— space-separated list of canonical chromosomes -
resources/blacklistFa/hs1_chrR.blacklist.fa.gz— blacklist FASTA (LFS-tracked) -
resources/tssBed/hs1_chrR_tssbeds.tar.gz— per-gene TSS bins (LFS-tracked); reused fromhs1_tssbeds.tar.gz -
resources/frip/hs1_chrR.DHS.bed.gz— DHS regions (LFS-tracked); reused fromhs1.DHS.bed.gz -
resources/frip/hs1_chrR.promoters.bed.gz— promoter regions (LFS-tracked); reused fromhs1.promoters.bed.gz -
resources/frip/hs1_chrR.enhancers.bed.gz— enhancer regions (LFS-tracked); reused fromhs1.enhancers.bed.gz
3. Register LFS tracking (.gitattributes)
Add LFS filter lines for all new binary/gz resource files, mirroring the hs1 entries:
resources/blacklistFa/hs1_chrR.blacklist.fa.gz filter=lfs diff=lfs merge=lfs -text
resources/frip/hs1_chrR.enhancers.bed.gz filter=lfs diff=lfs merge=lfs -text
resources/tssBed/hs1_chrR_tssbeds.tar.gz filter=lfs diff=lfs merge=lfs -text
resources/frip/hs1_chrR.DHS.bed.gz filter=lfs diff=lfs merge=lfs -text
resources/frip/hs1_chrR.promoters.bed.gz filter=lfs diff=lfs merge=lfs -text
✅ All entries added to .gitattributes and committed.
4. config/config.yaml
Add the hs1_chrR genome stanza (same HUMAN motifs as hs1):
hs1_chrR:
indexdir: "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs1_chrR/indexes"
blacklistFa: "$PIPELINE_HOME/resources/blacklistFa/hs1_chrR.blacklist.fa.gz"
chroms: "$PIPELINE_HOME/resources/chroms/hs1_chrR.chroms"
tssBed: "$PIPELINE_HOME/resources/tssBed/hs1_chrR_tssbeds.tar.gz"
homermotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_mono_homer_format_0.001.motif"
mememotif: "$PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz"
effectiveGenomeSize: 3000000000 # confirm actual value for chrR subset
fripextra:
dhsbed: "$PIPELINE_HOME/resources/frip/hs1_chrR.DHS.bed.gz"
promoterbed: "$PIPELINE_HOME/resources/frip/hs1_chrR.promoters.bed.gz"
enhancerbed: "$PIPELINE_HOME/resources/frip/hs1_chrR.enhancers.bed.gz"5. bin/aspen
Add hs1_chrR to the SUPPORTED_GENOMES variable (line ~65):
SUPPORTED_GENOMES="hg19 hg38 mm10 mmul10 bosTau9 hs1 hs1_chrR"6. config/config.yaml — user-facing comment
Uncomment/add hs1_chrR to the example genome comment block near line 30:
# genome: "hs1_chrR"7. Documentation
- Update
docs/(e.g.,docs/introduction.mdordocs/overview.md) to lisths1_chrRas a supported genome. - Add
CHANGELOG.mdentry under## development version.
Notes
hs1_chrRinherits HUMAN motif files fromhs1; no new motif files are needed.effectiveGenomeSizeshould be confirmed once the chrR-subset FASTA is assembled (thehs1value of 3,000,000,000 is a reasonable starting point but may differ for the canonical-chromosome subset).- frip and tssBed files for
hs1_chrRreuse thehs1originals (see reuse decision comment below).
Requested by
- @wuy24 — project CCRTEGS6
⚡ Generated using AI ⚡
Activity
kopardev commentedon Aug 3, 2026
Source genome clarification
The specific genome version to be used for
hs1_chrRis the Human_hs1-rDNA_genome_v1.0 from:Repository: https://github.com/vikramparalkar/rDNA-Mapping-Genomes
What this genome is:
The hs1 (T2T-CHM13) assembly has been:
Relevant files from that repo:
Human_hs1-rDNA_genome_v1.0.tar.gz(972 MB)hs1-rDNA_v1.0.fa,hs1-rDNA_v1.0.fa.faiHuman_hs1-rDNA_genome_v1.0_annotation.tar.gzhs1-rDNA_v1.0.bedHuman_hs1-rDNA_genome_v1.0_control_tracks.tar.gzImplications for resource file creation (Task 1–2 above):
hs1-rDNA_v1.0.fa(not a plain hs1 FASTA).resources/chroms/hs1_chrR.chromsshould include all canonical hs1 chromosomes pluschrR.chrR-specific annotation BED (hs1-rDNA_v1.0.bed) should be used when building TSS/promoter/enhancer resource files; standard hs1 BED files should be filtered to exclude unmasked rDNA-like loci.effectiveGenomeSizeshould be recalculated from the masked+chrR FASTA (likely slightly lower than the unmasked hs1 value of 3,000,000,000).kopardev commentedon Aug 3, 2026
Resource file reuse decision
The following
hs1_chrRresource files will reuse the existinghs1files directly (symlink or copy), since the standard chromosomes and annotation content are identical betweenhs1andhs1_chrR— the only addition inhs1_chrRis thechrRchromosome:resources/frip/hs1_chrR.DHS.bed.gzresources/frip/hs1.DHS.bed.gzresources/frip/hs1_chrR.promoters.bed.gzresources/frip/hs1.promoters.bed.gzresources/frip/hs1_chrR.enhancers.bed.gzresources/frip/hs1.enhancers.bed.gzresources/tssBed/hs1_chrR_tssbeds.tar.gzresources/tssBed/hs1_tssbeds.tar.gzThese files do not need to be regenerated from scratch. Tasks 2 checklist items for these four files can be resolved by copying/symlinking the
hs1originals and committing them under thehs1_chrRnames via LFS.The
chrR-specific annotation BED (hs1-rDNA_v1.0.bedfrom the Paralkar repo) only needs to be incorporated if rDNA-region FRiP or TSS enrichment metrics are desired forchrRspecifically — that can be a follow-up enhancement.docs: add missing CHANGELOG entries for v13-feat container fixes