기타 스킬

Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

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Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.

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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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Use when users need bioinformatics analysis on the NCPGR cluster, especially when converting analysis requests into local software choices, resource plans, and LSF job scripts.

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Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.

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Use this skill when the user asks about CMV vehicle inspections under 49 CFR 396 — DVIRs (Driver Vehicle Inspection Reports), pre-trip inspections, post-trip inspections, periodic inspections, annual inspections, who can perform inspections, OOS criteria, and what makes a "no defect" DVIR valid. Cite 49 CFR 396.

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Use this skill when the user asks about oversize / overweight load permits — state-by-state permitting process, escort vehicle (pilot car) requirements, route surveys, federal axle weight limits (Federal Bridge Formula), holiday restrictions, multi-state permits, and how to determine if a load needs a permit. Reference state DOT permitting offices.

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Use this skill when the user asks about the financial differences between being an owner-operator vs company driver — gross pay, expenses, net pay, capital requirements, risk tolerance, lifestyle, and how to evaluate the path. Reference industry pay surveys.

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Use this skill when the user asks the cost of pulling a Motor Vehicle Record (MVR) in a specific state, or wants to compare MVR fees across multiple states, or is budgeting annual compliance costs for a multi-state fleet. Reference the canonical fee table below; flag that fees change (re-verify with state DMV before annual budget planning).

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Use this skill when the user asks about state-specific trucking taxes BEYOND IFTA — NY Highway Use Tax (HUT), KY Kentucky Intrastate Tax (KIT), Oregon Weight-Mile Tax, New Mexico Weight-Distance Tax, Connecticut Highway Use Fee, or other state-level road-use taxes for commercial vehicles. Covers thresholds, rates, registration, filing cadence, and how these differ from IFTA. Reference state DOT/DOR resources.

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Use this skill when the user asks about team driving — two-driver OTR operations, how teams maximize miles, HOS rules with sleeper berth swap, pay structures, equipment requirements (sleeper berth specs), team retention, and common challenges. Reference 49 CFR 395.1(g).

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Use when a carrier asks how to spec a new tractor — engine choice (X15 vs DD16 vs PACCAR MX), transmission (manual vs automated manual vs automatic), axle ratio, sleeper size, fuel tanks, aerodynamic options, electronic features, warranty, fleet-spec vs premium-spec tradeoffs, and how spec choices affect resale value.

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Use when a carrier asks about trailer types — dry van, reefer, flatbed, step-deck, conestoga, tanker, dump, lowboy, intermodal chassis, auto-hauler. Covers length / weight rules, common specs, reefer unit options (Carrier vs Thermo King), liftgate options, kingpin setting, and trailer-to-tractor matching.

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Use this skill when documenting supervisor reasonable-suspicion training for Part 382 compliance. Covers what to log, what to retain, and what training providers to use.

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Use this skill to understand defensive driving course expectations for CMV drivers. Covers federal vs state vs carrier-specific requirements.

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Use this skill for record retention after a driver leaves your employment. Covers when records can be destroyed vs retained for cause.

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Use this skill when buying a used tractor or trailer. Covers verifying compliance status, hidden issues, and what to inspect before signing.

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Use this skill to understand trailer-specific inspection requirements when a trailer is not coupled to a tractor. Covers annual inspection, DVIR rules, and parking inspections.

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Use this skill for vehicle brake system inspection requirements. Covers daily DVIR, weekly maintenance, brake adjustment check, and the 'percent of out-of-adjustment' rule.

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Use this skill when selecting a TPR-registered Training Provider for behind-the-wheel ELDT training. Covers the registry, evaluation criteria, and common pitfalls.

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Use when a carrier is evaluating ELD / telematics / dashcam platforms and needs an objective comparison of Samsara, Motive (formerly KeepTruckin), and Geotab. Covers ELD compliance, AI dashcams, driver scoring, integrations, pricing structure, and which fleet profile suits which platform.

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Use this skill when the user asks about refrigerated (reefer) trucking — cold chain compliance, FDA temperature recording requirements, Sanitary Transportation Rule (STR / 21 CFR 1.900-1.934), commodity-specific temperature ranges, refrigeration unit operation, temperature recorder calibration, and how a load is challenged if temperature deviates. Cite 21 CFR Part 1 Subpart Q.

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Use this skill to understand record retention requirements for currently-employed drivers. Covers DQF, HOS, vehicle records, and D&A specific periods.

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