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This skill performs A/B compartment shift analysis between two Hi-C samples.
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| name | hic-compartment-shift |
| description | This skill performs A/B compartment shift analysis between two Hi-C samples. |
This skill performs A/B compartment shift analysis using PC1 eigenvector values extracted from Hi-C data, following the HOMER framework. It supports two conditions, each with two or more replicates, and uses the PC1 values (E1 column) from user-provided TSV files.
Major steps include:
Use this skill when you want to:
Example input set:
CT1_rep1.tsvCT1_rep2.tsvCT2_rep1.tsvCT2_rep2.tsvAdditional requirements:
compartments_shift_analysis/
shift_regions/
diff_PC1_CT2_vs_CT1.txt
regions.*.txt # other region files output by the tools used.
temp/
bins_PC1.txt
PC1_all_samples.txt
*.bedGraph # other bedGraph file
awk 'BEGIN{OFS=" "} NR>1 && NF==5 {print $1, $2, $3, $5}' CT1_rep1.tsv > CT1_rep1.PC1.bedGraph
Use any one TSV as the template:
awk 'BEGIN{OFS=" "} NR>1 && NF==5 {print $1, $2, $3}' CT1_rep1.tsv > bins_PC1.txt
The resulting bins_PC1.txt defines genomic intervals for PC1 extraction.
Call:
mcp_homer-tools__homer_differential_PC1with:
bins_pc1_path: Path to the bins_PC1.txt file generated earlier,genome: HOMER genome identifier, provided by user.bedgraph_paths: List of PC1 bedGraph files in the exact replicate order (e.g., CT1_rep1, CT1_rep2, CT2_rep1, CT2_rep2).experiment_labels: List of experiment group labels matching bedGraph order (e.g. ['CT1','CT1','CT2','CT2']).merged_output_path: Output path for merged PC1 table. Empty → '<bins_pc1_path>.merged_PC1.txt'.diff_output_path: Output path for differential PC1 table. Empty → 'diff_PC1.txt'.