Export a complete processed ABIF trace region
Choose sample or basecall bounds, check channel binding and stored anchors, and save complete region SVG, CSV, all call qualities and the original.
Select one supported original
Choose exactly one ABIF/AB1 file, up to 16 MiB. This finite ABIF101 profile needs processed DATA9–12, FWO_1, PBAS2 and PLOC2; optional PCON2 supplies call quality. It does not interpret raw dye channels or recalculate calls. A filename extension is only a picker hint.
The file may contain up to 5,000 directory entries, 500,000 points per channel and 40,000 calls. Ordered directory metadata and payload hashes remain in the report; unknown payload bytes stay in the exact original. The four processed channels must be equal-length and bound through the actual FWO_1 order.
Choose the coordinate system before the numbers
Samples means zero-based inclusive array indices. Bases means one-based inclusive PBAS2 call positions. For a base range the first and last stored PLOC2 anchors define the sample range; no extra flank is invented. Enter safe-integer start/end, end at least start, within the selected file.
The limit is 8,000 selected samples, not 8,000 basecalls. A short basecall range can span more samples than expected; check the resolved sampleStart/sampleEnd and selectedPoints. Defaults request samples 0–499 and do not silently shorten a smaller file.
| Choice | Start origin | Inclusive end | Delivered samples |
|---|---|---|---|
| Samples | 0 | Yes | Every array index from start through end |
| Bases | 1 | Yes | Every sample between the two stored PLOC2 anchors |
Check a synthetic range and quality distinction
The included synthetic-trace.ab1 is a 1,378-byte synthetic file with 128 points per channel, 16 calls and qualities 20–35. Samples 0–7 retain all eight rows below and include only call 1 (A, anchor 4, quality 20); all 16 calls remain in the report and basecalls.csv. It is not the forum author’s attachment or an experimental chromatogram.
The first three calls are A@4, C@12 and G@20, so bases 1–3 resolve to samples 4–20 inclusive: 17 points. The default end=499 is invalid for this 128-point demo; loading the example explicitly sets 0–7 without truncating a default range.
PBAS2 may contain uppercase IUPAC ambiguity symbols; they remain labeled. PCON2 values range from 0 to 255. If PCON2 is absent, each quality is null and CSV quality cells are empty. A stored zero stays 0 and must not be mistaken for absence.
sample_index,A,C,G,T
0,16,-12,-12,-12
1,34,-12,-12,-12
2,52,-12,-12,-12
3,70,-12,-12,-12
4,88,-12,-12,-12
5,70,-12,-12,-12
6,52,-12,-12,-12
7,34,-2,-12,-12
Keep the full selected curve and all original calls
Every trace-NNN.svg page includes at most 500 selected sample positions and all four channel coordinates. No sample is thinned, smoothed or clipped. All pages share the selected signed domain including zero; a one-sample selection gets four visible markers. Labels refer to stored calls whose anchors fall inside that page.
Download every page and both CSV files. samples.csv contains every selected index with A/C/G/T values, while basecalls.csv retains all original calls and qualities, including calls outside the displayed region. Full report copy is byte-identical to report.json; a limited preview is not the complete dataset.
| File | What remains complete |
|---|---|
| report.json | Source/hash, directory, channel binding, selection, all calls and every selected sample |
| samples.csv | Every selected sample index and A/C/G/T value |
| basecalls.csv | All source call positions, bases, anchors and qualities |
| trace-NNN.svg | Every selected point and in-range anchored call label across all pages |
| original.input | All original bytes, including opaque tags |
- Confirm samples versus bases before checking the resolved sampleStart, sampleEnd and selectedPoints in report.json.
- Check the actual FWO_1 channel binding and stored PLOC2 call anchors; distinguish a missing PCON2 quality from a stored zero.
- Download every trace-NNN.svg page, samples.csv, basecalls.csv, report.json and original.input; calls outside the displayed range remain in the complete call export.
- After cancellation or timeout, rerun the same retained original File and range parameters. For a range refusal, inspect its bounds and choose a valid range explicitly.
Recover with the original still selected
For a range refusal, inspect the file’s coordinate bounds and choose a smaller valid range. For a format or payload refusal, use a reader that supports that file; renaming it or treating raw channels as processed does not fix the source. Complete files plus report text are capped at 32 MiB without shortening fields.
One 10-second deadline includes file reads, loading, processing, result validation and first display. Cancellation or timeout leaves no partial or late result; retry the same original File and parameters after stopping. Contents and filenames stay in the browser without persistent source storage. The finite processed profile does not certify the complete ABIF standard or interpret biological results.
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.