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How to use the Mem-seq browser

Mem-seq combines membrane crosslinking with high-throughput sequencing to identify which DNA and RNA molecules interact with the bacterial envelope. Use the tools in this explorer to analyze coverage profiles, peak clusters, and meta-peak structures around membrane-associated loci.

This page explains how Mem-seq data are visualised and how to interpret the main views. All text is intentionally high-contrast for readability.

1. Input files

For each dataset, the browser expects the following files in the dataset folder (for example data/memseq/run10):

  • BigWig coverage in bigwig/*.bigwig for DNA/RNA tracks.
  • Annotations in annotations.csv with columns:
    gene_name,start,end,feature_type,strand,locus_tag,chromosome
  • Normalization factors (optional) in norm_factors.json to scale each track to 10M reads.
  • Summit clusters in summits_with_gene_localization_yffs.bed (chrom, start, end, name, cluster, gene_name, localization).

2. Coverage view

The Coverage page plots multiple BigWig tracks around a chosen gene.

  • Use the gene name box to type any annotated gene (e.g. yffS) and click Go.
  • The window slider sets the region around the gene (±1–50 kb).
  • The spacing slider controls vertical distance between tracks.
  • Black bars mark genes on the + strand, grey bars mark genes on the − strand, and purple bars label tRNA/hkRNA features.
  • Vertical shaded bands show summits coloured by cluster (1–3).

3. Cluster view

The Clusters page (once configured) summarises peaks grouped by their genome-wide profiles.

  • Each cluster shows a meta-profile over all summits in that group.
  • Heatmaps display individual peak behaviour across tracks, ordered by cluster.
  • Tables summarise enrichment for protein localization categories and GO cellular component terms.

4. Adapting to your own data

To apply the Mem-seq browser to another run, create a new dataset folder under public/data/memseq/, copy your BigWig and annotation files, and update memSeqConfig.ts with the new dataset name and track list. Vercel will then serve the files directly from thepublic directory.