track-generation
Installation
SKILL.md
Overview
This skill converts filtered BAM files into normalized signal tracks (BigWig) for genome browser visualization.
It supports both ATAC-seq and ChIP-seq datasets, automatically detecting genome assembly and chromosome size files.
Main steps include:
- Refer to the Inputs & Outputs section to check inputs and build the output architecture. All the output file should located in
${proj_dir}in Step 0. - Always use filtered BAM file (
*.filtered.bam) if available. - Normalize all tracks to 1 million mapped reads (RPM normalization).
- Generate the chrom.size file.
- For ATAC-seq, apply Tn5 offset correction (+4/−5) and generate normalized BigWig (RPM).
- For ChIP-seq, generat RPM-normalized track without applying Tn5 offset correction
- Always prompt user for whether need to visualize the signal profiles around TSS or target regions.
- Visualize the signal profiles around TSS or target regions if users require.