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Document that ultima_fastq requires no poly(A) - #91
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Ultima-delivered FASTQs end 5 bp before the trimmed homopolymer, so the ultima_fastq platform must not depend on a detectable 3' poly(A). Checked: - R2_polyA_filter is false for both ultima_fastq blocks, so filter_R2 keeps every CB/UB-tagged alignment and filter_bam.py is skipped. - starsolo_R2 always runs STAR with --clipAdapterType CellRanger4. On simulated Ultima-style R2 reads (both strands, ending in plain sequence, just before a genomic A-run, or 1-12 bases into one) STAR kept every aligned 3' end exact; it only clipped reads whose last 30 bases were A's, which Ultima's homopolymer trimming does not produce. No code change is needed; chemistry.yaml, AGENTS.md and the README now say so explicitly. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Summary
Confirms, and documents, that the
ultima_fastqplatform does not require a detectable 3' poly(A) at any step. Docs only; no code change was needed.What was checked
ultima_fastqblocks (chromiumV3, chromiumV4) setR2_polyA_filter: false, sofilter_R2keeps every CB/UB-tagged alignment and skipsfilter_bam.py.starsolo_R2always runs STAR with--clipAdapterType CellRanger4, which can clip a 3' poly(A). Simulated Ultima-style R2 reads were aligned with the exactstarsolo_R2flags (STAR 2.7.11b), with CellRanger4 and with clipping off (Hamming, no adapter):Only the last case changes, and Ultima's homopolymer trimming removes such tracts, so real
ultima_fastqreads keep their true end (the +5 bpR2_priming_offsetthen gives the priming site).Changes
chemistry.yamlcomment, AGENTS.md configuration notes and the README's Ultima notes now say explicitly that no poly(A) is required.🤖 Generated with Claude Code