Automate peak calling from BAM files for ChIP-seq and ATAC-seq experiments.
npx skills add https://github.com/BIsnake2001/ChromSkills --skill peak-calling
Please help me install this Agent Skill. Skill: peak-calling Source: https://github.com/BIsnake2001/ChromSkills/tree/main/3.peak-calling Command: npx skills add https://github.com/BIsnake2001/ChromSkills --skill peak-calling
Automates peak calling from BAM files for ChIP-seq and ATAC-seq experiments.
Run the peak-calling skill in a project directory containing BAM files to automatically generate peak calls and logs.
High-intent search queries and answers about installing and using this skill.
MACS3 peak calling is automated by running the skill in a directory containing BAM files, which auto-detects experiment type and generates peaks, logs, and a parameter log.
Narrow or broad peak mode is auto-detected for ChIP-seq data. The skill automatically determines the appropriate peak mode based on the input BAM files.
Filtered BAM files are automatically used for ATAC-seq peak calling when available. The skill detects single- or paired-end sequencing and applies specialized ATAC-seq parameters.
ChIP-seq peak calling requires user-supplied genome size and q-value. The skill dynamically prompts for these parameters and required control files before processing.
Both single-end and paired-end sequencing data are supported. The workflow auto-detects the sequencing type from the BAM files to apply the correct MACS3 parameters.
The MACS3 peak calling workflow generates peak files, processing logs, and a parameter log detailing the chosen options. This creates a reproducible results trail for your experiments.
ovachieverRead and write SAM/BAM/CRAM alignments and VCF/BCF variants using pysam.
jaechang-hitsRetrieve TF binding profiles from JASPAR 2024 and scan DNA sequences for TFBS.
BIsnake2001Merges BAMs and generates pseudo-replicates for reproducible peak analysis.
zongtingweiAutomate ChIP-seq peak calling, annotation, and motif analysis with MACS3.
