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Track merged guides, fix the measured-gene lookup, and carry the annotation tables - #15
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Two library entries of one spacer are one feature in any reference built on the spacer, and their reads land together. This library has 12 such pairs, each a 20-mer and the same spacer with a 5' G added for U6 transcription. They cannot be separated, and not for want of a better reference: the leader ends in a poly-G run, so the extra base is indistinguishable from the leader's own, and splitcode extracts a fixed 20 nt anchored on the scaffold, which both entries yield identically. Cell Ranger keeps all 43,778 features and assigns the 21-mer zero reads in every one of the 12 pairs; its counts for those guides are the 20-mer's alone. So the spacer stays what the reads can resolve, and the table says which guides carry a sum: `oligo` records what was ordered, `n_oligos` how many entries share the spacer. Above one, a guide is not comparable with one ordered once. Both columns travel into guide_metadata.tsv. Measured on the hiPSC-to-EC library: 24 entries flagged over 12 spacers, and 33,164 of 43,778 entries carry an extra 5' base, so oligo differs from spacer for three quarters of the library. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
chr:start-end is what a genome browser takes, and a browser is 1-based, so an element named that way starts one base after the BED row it came from. A pairs table that concatenated the BED's own columns is 0-based, and the exact string match between them found nothing: all 26 validated enhancers of the hiPSC-to-EC library carried no putative_target_genes, silently, until someone asked where the target genes had gone. The lookup now falls back to that one offset. Only that direction: the reverse does not arise from the convention and would risk matching the element next door. On the library, 180 of 340 enhancer guides gain a gene. The other 160 are 14 elements the BED marks e2g_validated but which have no row in the pairs table, so their genes are missing from the source rather than from the join. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
guide.var holds the IGVF columns, and the signed distances, promoter transcripts and other-gene-type overlaps were nowhere in the object. They cannot go in var either: guide_gene_annotation.tsv is one row per guide per site per gene, 45,501 for 43,766 guides, and collapsing it would force a rule on multi-site guides that nothing downstream asked for. So both tables are carried whole in mod['guide'].uns, by --guide-annotation and --element-mapping. Nothing is decided; the rows are there to be joined. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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Three things, each its own commit.
oligoandn_oligosTwo library entries of one spacer are one feature in any reference built on
the spacer, and their reads land together. This library has 12 such pairs,
each a 20-mer and the same spacer with a 5' G.
They cannot be separated, and not for want of a better reference. The leader
ends in a poly-G run, so the extra base is indistinguishable from the
leader's own, and splitcode extracts a fixed 20 nt anchored on the scaffold,
which both entries yield identically. Cell Ranger keeps all 43,778 features
and assigns the 21-mer zero reads in all 12 pairs -- its counts for those
guides are the 20-mer's alone, so the extra feature buys nothing.
So
spacerstays what the reads can resolve and the feature count stays43,766.
oligorecords what was ordered,n_oligossays how many entriesshare the spacer, and above one a guide is not comparable with one ordered
once. Both reach
guide_metadata.tsv, and soguide.var.Measured: 24 entries flagged over 12 spacers; 33,164 of 43,778 entries carry
an extra 5' base, so
oligodiffers fromspacerfor three quarters of thelibrary.
The measured-gene lookup
chr:start-endis browser notation and therefore 1-based, while a pairstable built from a BED's own columns is 0-based. The exact string match
between them found nothing, so all 26 validated enhancers carried no
putative_target_genes-- silently.180 of 340 enhancer guides now gain a gene. The remaining 160 are 14 elements
the BED marks
e2g_validatedthat have no row in the pairs table at all.The annotation tables in
guide.unsThe signed distances, promoter transcripts and other-gene-type overlaps were
nowhere in the MuData. They cannot go in
var: the annotation is one row perguide per site per gene, 45,501 for 43,766 guides. Both tables are now
carried whole under
--guide-annotationand--element-mapping, decidingnothing.
730 tests pass.
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