Appendix C — File formats
This appendix lists the files you can give EpiNexus and the main tables it writes, with their columns. Chapter 3 explains the common genomic formats.
C.1 Files you can upload
| Kind | File endings | Notes |
|---|---|---|
| Reads | .fastq, .fq, .fastq.gz, .fq.gz |
Single-end, or paired-end as two files (read 1 and read 2) |
| Alignments | .bam, with .bai or .bam.bai |
Sorted BAM files; upload the peak files beside them (EpiNexus calls peaks only from FASTQ) |
| Regions | .bed, .narrowPeak, .broadPeak (also .gz) |
Peaks, for runs that start from BAM files |
| Signal | .bedGraph, .bdg, .bigWig, .bw |
Signal tracks |
| Methylation | .cov, .cov.gz |
Bismark coverage files |
| Sample sheets and tables | .csv, .tsv, .txt |
Sample sheets |
Sample sheet. One row per sample, with the columns SampleID, fastq_r1, fastq_r2, Factor, Condition and Replicate (Chapter 4). Leave fastq_r2 empty for single-end reads. Factor is the target (for example H3K27ac), or input or IgG for a control.
C.2 Tables EpiNexus writes
All tables are in the run’s results and in the GEO submission package (Chapter 18). Coordinates are 0-based, half-open, as in BED files.
| File | One row per | Columns |
|---|---|---|
all_peaks.csv |
tested region (differential) | baseMean (mean normalised count), log2FC (shrunk), lfcSE, stat, pvalue, FDR, log2FC_mle (unshrunk), peak_id, direction, chrom, start, end, significant |
all_peaks.csv from csaw (broad marks) |
tested region | peak_id, chrom, start, end, log2FC (not shrunk), pvalue, FDR, baseMean (empty), direction, significant; no size_factors.csv and no normalised counts |
size_factors.csv |
sample | sample, size_factor |
counts_raw.tsv.gz |
region | region_id, chrom, start, end, then the read count of each sample |
counts_normalized.tsv.gz |
region | the same, with counts divided by the size factors |
<sample>_annotated.csv |
peak | chrom, start, end, name, score, peak_center, gene_id, gene_name, distance_to_tss, annotation, gene_strand |
GO_enrichment.<set>.csv |
GO term | ontology, term_id, term_name, region_hits, expected_hits, fold_enrichment, binom_p, binom_fdr (region test), genes_in_term, gene_hits, hyper_p, hyper_fdr (gene test), significant, genes |
differential_motifs.tsv |
motif and region set | set, motif_id, name, tf_class, tf_family, consensus, tp and tp_pct (regions with the motif), fp and fp_pct (control with the motif), enr_ratio, pvalue, qvalue, significant |
monalisa.tsv |
motif and fold-change bin | motif_id, name, bin, log2enr, negLog10P, negLog10Padj |
<sample>_super_enhancers.csv |
joined enhancer region | id, chrom, start, end, size, signal, rank, is_super, nearest_gene |
<sample>_links.csv |
enhancer–gene link | peak_id, chrom, start, end, element_class, is_self_promoter, gene_id, gene_name, gene_tss, distance, contact, activity, abc_score |
qc_report.csv |
sample | reads, mapping, duplicates, peaks, FRiP, complexity (NRF, PBC1, PBC2), cross-correlation (NSC, RSC), assay-specific metrics, spike-in metrics, and the QC verdict with its reasons |
Peak files from MACS3 follow the narrowPeak format: chromosome, start, end, name, score, strand, signal value, −log10 p-value, −log10 q-value and the summit’s position within the peak (Chapter 7).