Results for “dedup”

Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.

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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for visualisation.

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Import leads into a CRM with dedup, scoring and consent checks, approval-gated. "dedupe and score this lead list"

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Parses and processes SARIF files from static analysis tools like CodeQL, Semgrep, or other scanners. Triggers on "parse sarif", "read scan results", "aggregate findings", "deduplicate alerts", or "process sarif output". Handles filtering, deduplication, format conversion, and CI/CD integration of SARIF data. Does NOT run scans — use the Semgrep or CodeQL skills for that.

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Use when a broad paper candidate pool needs deterministic deduplication and a stable core set.

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Merges, appends, joins, and deduplicates multiple CSV, TSV, and Excel files (including multi-sheet workbooks) with pandas - mapping mismatched column names to one schema, normalizing keys, resolving conflicting values, tracking which file each row came from, and verifying the row math. Use when the user wants to combine spreadsheets or exports, stack monthly files, consolidate contact or lead lists, VLOOKUP-style join two sheets on an ID or email, or dedupe records across sources, even if they only say "put these together" or "clean up these lists into one".

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Analyzes test suites to identify redundant and duplicate test cases using coverage analysis, semantic similarity, and execution results. Use this skill when you need to reduce test suite size, identify redundant tests, optimize test execution time, analyze test coverage overlap, find tests with identical behavior, or improve test suite maintainability. Triggers when users ask to deduplicate tests, find redundant test cases, reduce test suite size, identify duplicate tests, or optimize test coverage.

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Design a data cleaning and transformation pipeline — missing values, outliers, and deduplication. Use when asked to "clean this dataset", "handle missing values", or "deduplicate this data".

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BorgBackup (Borg) is a deduplicating backup program with optional compression and authenticated encryption. It uses content-defined chunking for space-efficient daily backups, making it ideal for automating secure incremental backups to local or remote SSH targets.

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Manage an engagement buffer that ingests, prioritizes, rate-limits, deduplicates, and tracks state for incoming engagement items across platforms. Generates periodic digests and enforces cooldown periods. Composes with du-dum: du-dum sets the observation/action cadence, this skill manages the queue between beats.

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Use when designing, reviewing, or troubleshooting Salesforce duplicate prevention, matching rules, duplicate rules, and merge governance. Covers cleaning up duplicates that already exist at ordinary volume: merge sequencing, survivorship, stewardship ownership. Also covers the deployable MatchingRule / DuplicateRule metadata, the Alert-vs-Block action pair, DuplicateRecordSet reporting, and the Apex DMLOptions.DuplicateRuleHeader.allowSave bypass. Triggers: 'duplicate rule', 'matching rule', 'merge strategy', 'dedupe', 'survivorship', 'D&B', 'same contact twice', 'clean up duplicate records', 'clean up duplicate accounts', 'DUPLICATES_DETECTED', 'allowSave', 'FindDuplicates'. NOT for cleanup at volume — hundreds of thousands of records, batch merge jobs, DemandTools/Cloudingo — use data/large-scale-deduplication. NOT for which field values and child records the platform keeps in a merge - use data/record-merge-implications.

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Audit server-side paid-media measurement including server-side tag management, platform conversion APIs, event taxonomy, browser/server deduplication, consent, hashing, data quality, observability, and privacy. Use for server-side tracking, sGTM, server-side tagging, Meta CAPI, TikTok Events API, event_id, deduplication, pixel debugging, first-party measurement, or conversion data loss.

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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for visualisation.

The English summary is being prepared. Showing the original description.

Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.

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A pessimistic go/no-go the moment you pick up a GitHub issue — read it skeptically and hunt for reasons NOT to do it (already done? obsolete? duplicate? premise wrong? cheaper way? net-negative?), returning proceed / reshape / drop with one-line evidence. The pickup-time half of the dedup gate (the create-time half is /issue-dedup). Use as step 1 of the Task Execution Workflow, or run /issue-sanity-check

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Deploy DefectDojo as a centralized vulnerability management dashboard with scanner integrations, deduplication, metrics tracking, and Jira ticketing workflows.

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Use when the user asks to "QA my conversion tracking before launch", "check my UTMs / pixel / event firing", "set up a tracking pre-flight", or "set the dedup rule so Meta and Google stop double-counting"; builds and fixes the measurement plumbing — conversion-event firing, UTM hygiene, cross-platform dedup rules, attribution-window alignment, and offline/iOS-ATT modeled-gap flags — as a pre-flight checklist plus a UTM/event-spec builder. Not for scoring R1/R2 — that is a scored veto in ad-account-auditor; not for account structure — use campaign-architect. 付费广告转化追踪QA/UTM规范/跨平台去重

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Create an Estuary derivation with custom SQLite state (internal tables) to make per-document decisions based on accumulated history — account balances, inventory levels, approval workflows, deduplication. Derivations add complexity and cost — confirm the user wants a derivation before reaching for this. Use when user says "stateful derivation", "derivation to track balance", "transformation to approve based on state", "derive an approval workflow", "deduplication derivation", or "build a stateful derivation".

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Deploy DefectDojo as a centralized vulnerability management dashboard with scanner integrations, deduplication, metrics tracking, and Jira ticketing workflows.

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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

The English summary is being prepared. Showing the original description.

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq c_curve / lc_extrap, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

The English summary is being prepared. Showing the original description.

Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

The English summary is being prepared. Showing the original description.

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq c_curve / lc_extrap, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

The English summary is being prepared. Showing the original description.