Inter-arm alignment

In the app

Analysis panel, under 2D tasks: Inter-arm alignment

Command

chromosomix interarm

Reads

A contact map

Also known as

arms, secondary diagonal, bacteria, SMC, ParB

Where SMC, loaded at parS beside the origin, zips the two arms of a bacterial chromosome together, its map carries a second diagonal through the origin. Inter-arm alignment turns that diagonal into numbers: how strongly the arms are held together, and how far from the origin.

Running it

The arms are read from the origin: in the Chromosomes table, the first step of the breadcrumb (Moving around), tick the sequence’s circular box and type its origin, 1-based, or let Origin and terminus fill it in. Until then the origin is the first base, and the drawer says so.

Then choose Inter-arm alignment in the 2D tasks card of the Analysis panel (4) and press run. It makes Inter-arm enrichment, a track marked * on the Tracks card of the Annotations panel: how much each locus touches its mirror image, in log2. The curves and the table below are in the drawer.

The same run from a shell, where --circular and --origin declare what the Chromosomes table holds:

chromosomix interarm <map> [--<parameter> <value> …] --out <dir>

chromosomix interarm ecoli.mcool::/resolutions/5000 --circular NC_000913.3 \
  --origin NC_000913.3:3925744 --out results/

Parameters

band is how close to the secondary diagonal a cell must be to count, in bins either side; 0 is the diagonal alone. window along the arms is used only by the control, after detrend.

Parameter	Takes	Default	What it does
sequences--sequences <name,…>	sequence names, comma-separated	Every sequence of the file when left out.	—
band--band <n>	a whole number, 0 to 50, in bins	2	Cells this close to the secondary diagonal are averaged; 0 is the diagonal alone.
window along the arms--armWindow <n>	a whole number, at least 0, in bins	50	For the enrichment after detrend: each cell is compared within this far along the arms, as the map’s arms and Compartments do; 0 is the whole chromosome.
use balancing weights--no-balance	a switch	On wherever the file carries balancing weights; --no-balance reads the raw counts.	—

What it writes

• curve: a curve: TSV
• profile: a value per bin: TSV, bedGraph and bigWig
• table: a table: TSV

On the command line every file goes into --out as <file stem>.interarm.<output>.<ext>, and each TSV opens with # lines naming the build, the file and every parameter that produced it.

Reading the result

Each cell is divided by the sequence’s own distance decay, and the log2 averaged within band bins of the secondary diagonal by distance from the origin: Inter-arm alignment by distance from the origin, a curve per sequence. Near the origin and the terminus, where the diagonals meet, cells nearer the main diagonal than twice the band and two bins are left out: they measure compaction, not alignment.

On the curve, 0 is no alignment: mirror images touch as often as any two loci as far apart. An aligned chromosome stands above 0 out from the origin, and falls back where the alignment ends. The same after detrend shares its axis. Contact decay along the diagonal and along both arms draws the two decays: along the diagonal, the short way round a circle, for the curve; within and across the arms for the control.

The table

Inter-arm alignment per sequence has a row per chromosome:

• read as circular or linear, and the origin used, 1-based.
• enrichment: how many times as often mirror images touch as expected, from the origin out to the reach; 1 is no alignment, 2 twice as often. Where nothing reaches, it is the whole arm’s.
• enrichment after detrend: the same cells over the decay along both arms, which absorbs the secondary diagonal: a control on that detrending, near 1 where it works, not a second measure.
• reach: how far from the origin, in base pairs, the enrichment holds before it falls four-fifths of the way from its peak back to 1 on a log scale, read from a running mean over 2 % of the arm.
• arm: the length of the longer arm.

As a guide, Pseudomonas aeruginosa, whose arms are aligned, reads 3.1 to 3.2 at 2 to 16 kb, reaching about 3.0 Mb of its 3.2 Mb arms, and 0.93 to 0.97 after detrend. E. coli, whose arms are not, reads 1.20 to 1.22: not exactly 1, because the stretch read is wherever its noise runs highest.

What to watch for

• Declare the circle. A chromosome read as linear, with its origin near either end, has one arm; the drawer says so.
• Size. A chromosome over 8,192 bins is left out and named: open the file at a coarser resolution. One under 8 bins is left out too.
• Comparing libraries. On a deck, run on all N maps brings the tables together, with a column naming each row’s map (Maps side by side).