bio-clip-seq-clip-preprocessing
Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.
npx skills add BioTender-max/awesome-bio-agent-skills --skill clip-preprocessing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: umi_tools 1.1.5+, cutadapt 4.6+, fastp 0.23.4+, samtools 1.19+, pysam 0.22+, picard 3.1+, preseq 3.2+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # CLIP-seq Preprocessing **"Preprocess raw CLIP reads into UMI-deduplicated, alignable FASTQ"** -> Extract random barcodes, trim adapters without disturbing the 5' truncation site, length-filter to remove unmappable shorts, and (post-alignment) collapse PCR duplicates by UMI + position. The 5' end of the read carries the iCLIP/eCLIP truncation signature one base downstream of the protein-RNA crosslink; preserving this base is the single most important constraint of CLIP preprocessing. - CLI (eCLIP, paired-end): `umi_tools extract --bc-pattern=NNNNNNNNNN --stdin R1.fq.gz --read2-in R2.fq.gz --stdout R1_umi.fq.gz --read2-out R2_umi.fq.gz` - CLI (iCLI
- Version Compatibility
- Read Structure by Protocol
- Critical Choice: One Adapter Pass vs Two
- Per-Protocol Failure Modes
- eCLIP -- 5' end trimmed by mistake
- iCLIP / iCLIP2 -- Demultiplex confusion with UMI
- PAR-CLIP -- T->C mistaken for sequencing error
- Quality trimming too aggressive
- Library complexity below threshold
- UMI Deduplication Decision
- Pre-Mapping rRNA Filter (Optional but Standard)
- Library Complexity Assessment
- QC Checkpoints After Preprocessing
- Common Errors
Pass 1 - 3' adapter (both reads) cutadapt \ R1.umi.fq.gz R2.umi.fq.gz Pass 2 - read-through 5' adapter on R2 only (ENCODE eCLIP) R1.p1.fq.gz R2.p1.fq.gz samtools index aligned.bam umi_tools dedup \ samtools index dedup.bam Pre-map to rRNA + repeats bowtie2 -x repbase_repeats -U R1.trim.fq.gz \
What does the bio-clip-seq-clip-preprocessing skill do?
Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill clip-preprocessing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.