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UPDATE the BED to cover the 5' base where the genome holds it - #21
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A U6 construct starts its transcript with a G, so a library is often ordered as G plus the protospacer. The G is there for the promoter, but a genome holding one pairs with it like any other base, and the site is then ten long rather than nine. The BED's interval now covers what pairs: one base longer where the 5' base does, and on the minus strand that moves end rather than start. The table's start and end stay on the declared protospacer, which spacer, target_site and guide_annotation's join are all built on, and a new paired_5p column says where the two differ. It has three states, so a library of bare protospacers says nothing rather than no, and so does a match that sat too close to a contig end to read the base under it. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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A U6 construct starts its transcript with a G, so a library is often ordered
as G plus the protospacer. That G is there for the promoter, not the design
-- but a genome holding one pairs with it like any other base, and the site
is then ten long rather than nine. The tool had no way to say which sites
those were.
guide_mapping.bed's interval now covers what pairs. One base longerwhere the guide's 5' base does; on the minus strand 5' is the higher
coordinate, so that moves
endrather thanstart. Verified against thereference bases on both strands: the widened interval reads
G+ the 9-mer.guide_genome_annotation.tsv'sstart/enddo not move.spaceriswhat they span,
target_siteis derived from them, andguide_annotationjoins on
guide_idplus the four site columns -- shifting them would breakthat join for every downstream table. The cut site does not move either way:
Cas9 cuts 3 bases 5' of the PAM, at the other end of the protospacer.
A new
paired_5pcolumn says where the two differ.TRUE,FALSE, orempty -- three states, because a library of bare protospacers has no such
base to ask about, and neither does a match sitting too close to a contig
end for the base under it to have been read. Empty is not no.
On 500 9-mers against chr21: 3,954 of 20,398 PAM-bearing sites pair, so the
BED holds 3,954 ten-base rows and 16,444 nine-base ones, and every row's
interval agrees with its table row to the base.
🤖 Generated with Claude Code