size_fragments
Read-only
Size the peaks of a fragment-analysis run (.fsa / .hid) against its own size standard, and hand them on as lengths in bases. A fragment run carries no sequence at all — dye channels and a ladder — so this is the node that turns one into numbers a pipeline can act on: allele sizes, a peak table, and the ladder's own measured accuracy beside them.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| kit | No | name each peak's locus and allele from a marker kit's own ladder definition. Left unset the node reports sizes, which is a complete measurement — a genotype needs a kit. Values: none (No kit — sizes only), file (A kit definition in this project), cordisplus (COrDIS Plus), cofiler (Cofiler), geneprint10 (GenePrint 10), globalfiler (GlobalFiler), identifilerlessils250 (Identifiler Less ILS250), identifilerpluslessils250 (IdentifilerPlus Less ILS250), identifilerplus (IdentifilerPlus), identifiler (Identifiler), microreaderyprime (Microreader Y Prime), minifiler (Minifiler), ngmselect (NGMSElect), ngm (NGM), niddkfragilex1 (NIDDKFragileX1), netbioflexplex (NetBio_FlexPlex), ppfusion6c (PowerPlex Fusion 6C), ppfusion-v2-6 (PowerPlex Fusion (v2.6)), ppfusion (PowerPlex Fusion), ppgeneprint24 (PowerPlex GenePrint24), pplexy23-v2-6 (PowerPlex Y23 (v2.6)), pplexy23 (PowerPlex Y23), powerplex1-2 (PowerPlex 1.2), powerplex16 (PowerPlex 16), powerplex18d-v2-6 (PowerPlex 18D (v2.6)), powerplex18d (PowerPlex 18D), powerplex21-v2-6 (PowerPlex 21 (v2.6)), powerplex21 (PowerPlex 21), powerplexs5 (PowerPlexS5), powerplexy (PowerPlex Y), powerplex-esi16-v2-6 (PowerPlex ESI16 (v2.6)), powerplex-esi16 (PowerPlex ESI16), powerplex-esi17-v2-6 (PowerPlex ESI17 (v2.6)), powerplex-esi17 (PowerPlex ESI17), powerplex-esx16-v2-6 (PowerPlex ESX16 (v2.6)), powerplex-esx16 (PowerPlex ESX16), powerplex-esx17-v2-6 (PowerPlex ESX17 (v2.6)), powerplex-esx17 (PowerPlex ESX17), profilerplus (ProfilerPlus), q-investigator24plex (QiagenInvestigator24plex), q-investigatorargusx12 (QiagenArgusX12), q-investigatorargusx12-qs (QiagenArgusX12_QS), ryanclarkecannabis (Cannabis), sefilerplus (SEfilerPlus), sgmplus (SGM Plus), yfilerplus (Yfiler Plus), yfiler (Yfiler), iplexstrliz500less250 (iPLEXSTRLIZ500less250), iplexstr (iPLEXSTR). | none |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| method | No | the sizing curve. Local methods use the standard fragments nearest each peak and are the more accurate on a real ladder; the global reciprocal fit is less affected by one standard fragment running anomalously. Applied Biosystems, DNA Fragment Analysis by Capillary Electrophoresis, Ch. 5. Values: local-southern (Local Southern), global-southern (Global Southern), least-squares-2 (Least squares (2nd order)), least-squares-3 (Least squares (3rd order)), cubic-spline (Cubic spline). | local-southern |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| document | No | which fragment file to read: its name (`ladder.fsa`) or its project file id. A file id is project-specific, so a template ships this unset. | |
| kit_file | No | which kit definition in this project, by file name or file id — for a kit this build does not bundle, which is the ordinary case for a regional or in-house panel. An OSIRIS `*_LadderInfo.xml`. Left empty when the project holds exactly one, it is used. Only read when `kit` is `file`. Only applies when kit is file. | |
| max_size | No | ignore peaks sized above this. In bases. | |
| min_size | No | ignore peaks sized below this. In bases. | |
| threshold | No | minimum peak height, in the channel's own units. | |
| ladder_dye | No | which dye carries the size standard. Left unset it is MEASURED, by matching the standard's own scans against each channel's peaks — the copy of the table in the file says nothing about which channel it ran in. Advanced. | |
| ladder_run | No | an ALLELIC LADDER of the same kit, in this project, to call against instead of the kit file's nominal sizes: its name (`identifiler-ladder.fsa`) or its file id. A kit's sizes are the manufacturer's own reference run, and yours reads them systematically long or short by length — measured on the bundled pairs, a ladder sits 0.27 bases from nominal at 175-200 and 1.40 at 300-325, and the sample beside it is off by the same amount, so comparing the two cancels what comparing to the table does not. Graded on the published 9947A profile over four kits: 24 of 42 loci exact against nominal, 35 of 44 against the ladder. A locus whose ladder does not produce all its declared alleles keeps its nominal sizes and says so rather than being labeled partly. Only applies when kit is file or cordisplus or cofiler or geneprint10 or globalfiler or identifilerlessils250 or identifilerpluslessils250 or identifilerplus or identifiler or microreaderyprime or minifiler or ngmselect or ngm or niddkfragilex1 or netbioflexplex or ppfusion6c or ppfusion-v2-6 or ppfusion or ppgeneprint24 or pplexy23-v2-6 or pplexy23 or powerplex1-2 or powerplex16 or powerplex18d-v2-6 or powerplex18d or powerplex21-v2-6 or powerplex21 or powerplexs5 or powerplexy or powerplex-esi16-v2-6 or powerplex-esi16 or powerplex-esi17-v2-6 or powerplex-esi17 or powerplex-esx16-v2-6 or powerplex-esx16 or powerplex-esx17-v2-6 or powerplex-esx17 or profilerplus or q-investigator24plex or q-investigatorargusx12 or q-investigatorargusx12-qs or ryanclarkecannabis or sefilerplus or sgmplus or yfilerplus or yfiler or iplexstrliz500less250 or iplexstr. | |
| lane_standard | No | the internal lane standard this run used, by its name (`ABI-LIZ-600-60-TO-460`, `Promega-ILS-600`, …). Only read when the FILE records no size standard of its own, which is every 3500 `.hid`: there the ruler has to be named because it was never written down. A `.fsa` carries its own table, which is a measurement of that run and always wins. NCBI OSIRIS's library, 133 standards across 24 families. | |
| allele_tolerance | No | how far a peak may sit from a ladder allele and still be called it. Above half the repeat unit (4 bases for most STR loci) a peak reaches two alleles and is reported as ambiguous rather than guessed. In bases. Only applies when kit is file or cordisplus or cofiler or geneprint10 or globalfiler or identifilerlessils250 or identifilerpluslessils250 or identifilerplus or identifiler or microreaderyprime or minifiler or ngmselect or ngm or niddkfragilex1 or netbioflexplex or ppfusion6c or ppfusion-v2-6 or ppfusion or ppgeneprint24 or pplexy23-v2-6 or pplexy23 or powerplex1-2 or powerplex16 or powerplex18d-v2-6 or powerplex18d or powerplex21-v2-6 or powerplex21 or powerplexs5 or powerplexy or powerplex-esi16-v2-6 or powerplex-esi16 or powerplex-esi17-v2-6 or powerplex-esi17 or powerplex-esx16-v2-6 or powerplex-esx16 or powerplex-esx17-v2-6 or powerplex-esx17 or profilerplus or q-investigator24plex or q-investigatorargusx12 or q-investigatorargusx12-qs or ryanclarkecannabis or sefilerplus or sgmplus or yfilerplus or yfiler or iplexstrliz500less250 or iplexstr. Advanced. | |
| min_peak_spacing | No | two maxima closer than this in one channel are one peak with a noisy top rather than two fragments: the separation is by length and no two fragments differ by less than one base. The taller is kept. 0 reports every maximum the detector finds. In bases. Advanced. | |
| pullup_threshold | No | a peak whose top sits inside the saturated top of a taller peak in ANOTHER dye, at or below this fraction of it, is named pull-up rather than called. Omitted, the kit's own published sample value from NCBI OSIRIS (0.2 for most kits; off where OSIRIS publishes none). 0 disables it. Only applies when kit is file or cordisplus or cofiler or geneprint10 or globalfiler or identifilerlessils250 or identifilerpluslessils250 or identifilerplus or identifiler or microreaderyprime or minifiler or ngmselect or ngm or niddkfragilex1 or netbioflexplex or ppfusion6c or ppfusion-v2-6 or ppfusion or ppgeneprint24 or pplexy23-v2-6 or pplexy23 or powerplex1-2 or powerplex16 or powerplex18d-v2-6 or powerplex18d or powerplex21-v2-6 or powerplex21 or powerplexs5 or powerplexy or powerplex-esi16-v2-6 or powerplex-esi16 or powerplex-esi17-v2-6 or powerplex-esi17 or powerplex-esx16-v2-6 or powerplex-esx16 or powerplex-esx17-v2-6 or powerplex-esx17 or profilerplus or q-investigator24plex or q-investigatorargusx12 or q-investigatorargusx12-qs or ryanclarkecannabis or sefilerplus or sgmplus or yfilerplus or yfiler or iplexstrliz500less250 or iplexstr. Advanced. | |
| stutter_threshold | No | the same test one repeat below rather than one base. 0.15 is OSIRIS's own StutterThreshold default, and the repeat unit is read off each locus's own ladder rather than typed in. 0 disables it. Only applies when kit is file or cordisplus or cofiler or geneprint10 or globalfiler or identifilerlessils250 or identifilerpluslessils250 or identifilerplus or identifiler or microreaderyprime or minifiler or ngmselect or ngm or niddkfragilex1 or netbioflexplex or ppfusion6c or ppfusion-v2-6 or ppfusion or ppgeneprint24 or pplexy23-v2-6 or pplexy23 or powerplex1-2 or powerplex16 or powerplex18d-v2-6 or powerplex18d or powerplex21-v2-6 or powerplex21 or powerplexs5 or powerplexy or powerplex-esi16-v2-6 or powerplex-esi16 or powerplex-esi17-v2-6 or powerplex-esi17 or powerplex-esx16-v2-6 or powerplex-esx16 or powerplex-esx17-v2-6 or powerplex-esx17 or profilerplus or q-investigator24plex or q-investigatorargusx12 or q-investigatorargusx12-qs or ryanclarkecannabis or sefilerplus or sgmplus or yfilerplus or yfiler or iplexstrliz500less250 or iplexstr. Advanced. | |
| require_resolvable | No | leave a peak unnamed when the neighboring allele is closer than twice THIS RUN's own sizing error at that length, instead of naming the nearest. Off by default: the error is measured with each size-standard fragment withheld, which is harsher than sizing a peak with all of them present, so in a sparsely anchored region it is pessimistic. On a run whose standard has a wide gap it is what stops a confident wrong allele; on an evenly anchored one it changes nothing. Every call carries the number either way. | |
| adenylation_threshold | No | a peak within one base of a taller one in the same locus, below this fraction of its height, is an incompletely adenylated shoulder of it rather than an allele. 0.3333 is NCBI OSIRIS's own AdenylationThreshold default. 0 calls every peak. Only applies when kit is file or cordisplus or cofiler or geneprint10 or globalfiler or identifilerlessils250 or identifilerpluslessils250 or identifilerplus or identifiler or microreaderyprime or minifiler or ngmselect or ngm or niddkfragilex1 or netbioflexplex or ppfusion6c or ppfusion-v2-6 or ppfusion or ppgeneprint24 or pplexy23-v2-6 or pplexy23 or powerplex1-2 or powerplex16 or powerplex18d-v2-6 or powerplex18d or powerplex21-v2-6 or powerplex21 or powerplexs5 or powerplexy or powerplex-esi16-v2-6 or powerplex-esi16 or powerplex-esi17-v2-6 or powerplex-esi17 or powerplex-esx16-v2-6 or powerplex-esx16 or powerplex-esx17-v2-6 or powerplex-esx17 or profilerplus or q-investigator24plex or q-investigatorargusx12 or q-investigatorargusx12-qs or ryanclarkecannabis or sefilerplus or sgmplus or yfilerplus or yfiler or iplexstrliz500less250 or iplexstr. Advanced. | |
| include_ladder_channel | No | also report the size standard's own peaks. They are the ruler, so they are excluded by default. Advanced. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| run | Yes | what the FILE says about itself: sample, instrument, polymer, dye names, scan count. Not the channels, which cannot ride a wire | |
| peaks | Yes | every sized peak: size in bases, dye, height, scan, and whether it saturated | |
| sizes | Yes | just the lengths in bases, ascending — the list a downstream gate reads | |
| alleles | Yes | each peak's locus and allele under the chosen kit, with the ones that could not be named and WHY. Null when no kit was named | |
| accuracy | Yes | this run's own sizing error in bases, measured by leaving each standard fragment out and sizing it from the others. A difference smaller than this is not one the run can resolve | |
| genotype | Yes | the alleles called per locus — the readout a downstream step compares. Null when no kit was named | |
| peakCount | Yes | how many peaks were sized | |
| sizeStandard | Yes | the ladder the sizes rest on: its fragments, the channel it was found in, and how that channel was chosen | |
| lane_standard_fit | Yes | how a NAMED lane standard was fitted, when one was used: the peaks it matched, the correlation it reached and the threshold that had to be cleared, so a caller can see why the sizes are trusted. Null for a run whose file records its own standard | |
| ladder_calibration | Yes | when a ladder run was named: which loci it labeled, at what spacing correlation, which it refused and why, and how many alleles were re-expressed in this instrument's own sizes. Null when the kit's nominal sizes were used |