Keep trace samples and basecall coordinates together
Distinguish sample indices, stored call anchors and missing quality so a selected chromatogram can be checked against its complete source.
A selected figure still needs its coordinate evidence
The original forum author clarified that only part of the chromatogram was needed for a manuscript. A reusable selected trace can retain exact samples and anchors while avoiding a giant whole-file image. The task is the region, but its source identity remains the complete AB1.
There was no actual author attachment. The included example is synthetic, and measured reader/fixture support establishes only this finite processed ABIF101 profile. It does not establish raw-channel or full-standard compatibility.
Samples and called bases describe different positions
Four processed channel arrays contain a value at each sample index. PBAS2 contains calls, and PLOC2 tells which stored sample anchors each call. Basecall position 2 therefore need not refer to sample index 2.
Use sample bounds when you need an exact array interval. Use base bounds when you want the interval between particular stored calls. Both endpoints are included; base positions start at 1 and sample indices at 0. No extra flank, smoothing or new call is added.
The synthetic demo’s first three calls are A@4 (quality 20), C@12 (21) and G@20 (22). Bases 1–3 therefore export samples 4–20, or 17 points; samples 0–7 export eight points and include only A@4. Both selections retain all 16 calls in the complete basecalls.csv. This small example is checked field by field against the included synthetic original, not an author attachment.
| Data | Coordinates | Meaning |
|---|---|---|
| Processed trace | Zero-based sample index | Stored A/C/G/T channel values |
| Basecall | One-based PBAS2 position plus PLOC2 anchor | Stored call and its sample anchor |
| Quality | Optional PCON2 entry for each call | Stored unsigned value; absence is null |
Missing quality is not a weak call
An absent PCON2 makes quality null; a present quality of zero stays zero. These values answer different questions about what the source contains. Retain them in the report and the complete basecall CSV rather than replacing missing quality with a number.
Ambiguous IUPAC calls remain in the output, with their original anchors and labels. The tool does not guess a clearer base from a channel peak. FWO_1 determines which of DATA9–12 maps to each A/C/G/T channel; the array order alone is not the evidence.
A vector figure and a screenshot have different uses
A screen capture records the visible view at a chosen pixel resolution. Complete SVG pages preserve every selected point and can be resized in a receiving editor. Keep the values as well as the vector image so geometry can be checked rather than judged only by appearance.
Every selected sample remains in samples.csv. All original calls remain in basecalls.csv and report.json even when their anchors fall outside the selected region. Saving original.input allows a different compatible reader to inspect the full file.
- Choose samples or bases first, then enter inclusive start/end.
- Check resolved sample bounds and selectedPoints before using the figure.
- Download all SVG pages and compare every selected sample with the CSV.
- Keep all call qualities, directory metadata and the exact original.
Make a smaller selection explicitly
A selection is limited to 8,000 samples and SVG pages to 500 samples each; full files plus report text are limited to 32 MiB. If a requested range is invalid or too large, it is refused instead of silently shortened.
Cancel or the 10-second full-operation deadline produces no partial or late figure. Retry with the same File and options, or document a deliberately smaller range. Processing stays in the browser, and the exported trace represents stored measurements without interpreting a sequencing experiment.
References
- zslee — a selected chromatogram region for a manuscript
The author explicitly wants part of the trace and accepts a higher-resolution method. No actual AB1 attachment was obtained; examples are synthetic.
- Biopython ABI reader
The measured reader and fixtures support the declared processed ABIF101 profile. A complete official ABIF specification was not obtained; this is not a full-standard or raw-channel compliance claim.
Tools in this category
Expand a tool to see its steps, options and supported formats, then open its workspace.
Processed ABIF trace regionExport every processed ACGT trace sample in a selected ABIF region, with stored basecall anchors, all qualities, complete SVG pages and exact source bytes.
Export every processed ACGT trace sample in a selected ABIF region, with stored basecall anchors, all qualities, complete SVG pages and exact source bytes.
Steps
- Select one original AB1/ABIF file.
- Choose sample or basecall coordinates and enter inclusive start/end; basecall positions begin at 1.
- Export the region and check actual sample bounds, channel binding and whether quality is present.
- Keep every SVG page, complete sample/basecall CSV, report and original; copy or download the full report.
Available options
- Coordinate range
- Sample indices (from 0) · Basecall positions (from 1)
- Start (included)
- 0
Minimum 0 for samples, 1 for basecalls.
- End (included)
- 499
Must be ≥ start and within the file; at most 8,000 selected samples.
Capabilities and limits
- Choose exactly one original file, up to 16 MiB, with a filename up to 512 UTF-8 bytes. The content must match the finite processed ABIF101 profile; a .ab1 extension alone does not establish support. Input and filename stay in the browser.
- Uses processed DATA9–12 signed 16-bit channels and the FWO_1 ACGT permutation, with PBAS2 calls and strictly increasing PLOC2 anchors. Optional PCON2 retains unsigned qualities 0–255; absent quality is null, distinct from zero. Raw channels, smoothing and guessed calls are not supported.
- At most 5,000 directory entries, 500,000 points per channel and 40,000 basecalls. The four channels must have equal nonempty lengths. Calls may contain supported uppercase IUPAC DNA symbols; ambiguous calls remain labeled instead of being changed to ACGT.
- Choose sample indices from 0, inclusive at both ends, or basecall positions from 1, inclusive at both ends. For a base range, the first and last stored PLOC2 anchors become the sample bounds; no flank is added. Start/end must be safe integers, end ≥ start, and within this file.
- Select at most 8,000 samples. Each trace-NNN.svg page contains at most 500 selected samples and every A/C/G/T coordinate, with no thinning or smoothing. Negative stored values remain visible; all pages share the selected signed signal range including zero. A single-sample selection has four visible channel markers.
- Download report.json, samples.csv, basecalls.csv, every trace-NNN.svg page and original.input. samples.csv contains the complete selection; basecalls.csv and the report retain all source calls and qualities, including those outside the range. The original keeps every opaque tag byte.
- Complete files plus full report text are limited to 32 MiB. The report includes ordered directory metadata and payload hashes, channel binding, exact selection and all selected samples. Full report copy is byte-identical to report.json; a bounded preview does not shorten exports.
- A single 10-second deadline includes source checks, file reading, loading, processing, validation and first result display. Cancel or timeout publishes no late or partial result; the same original file and parameters can be retried. This is a finite processed profile, not full ABIF-standard certification or medical interpretation.