refineTagsAndSort report
MiXCR generates a comprehensive summary of refineTagsAndSort command. Refine reports may be generated right along with refineTagsAndSort command using -r/--report for txt report and -j/--json-report for report in a json format, or can be exported using exportReports command.
Show sample report
============== Refine Report ==============
Analysis date: Sat Oct 01 08:42:50 CEST 2022
Input file(s): results/01a_d110_LN_germCenterB.vdjca
Output file(s): results/01a_d110_LN_germCenterB.refined.vdjca
Version: ; built=Mon Sep 26 10:55:18 CEST 2022; rev=8c998df1ab; lib=repseqio.v2.0
Command line arguments: --report results/01a_d110_LN_germCenterB.refine.report.txt --json-report results/01a_d110_LN_germCenterB.refine.report.json results/01a_d110_LN_germCenterB.vdjca results/01a_d110_LN_germCenterB.refined.vdjca
Analysis time: 4.19s
Time spent in correction: 1.71s
UMI input diversity: 11117
UMI output diversity: 1253 (11.27%)
UMI input reads: 87258
UMI output count: 82711 (94.79%)
UMI mean reads per tag: 7.85
UMI input core diversity: 1852 (16.66%)
UMI input core reads: 77675 (89.02%)
UMI directly corrected diversity: 5364 (48.25%)
UMI directly corrected reads: 5849 (6.7%)
UMI diversity filtered by tag quality: 4500 (40.48%)
UMI reads filtered by tag quality: 4547 (5.21%)
UMI diversity filtered by whitelist: 0 (0%)
UMI recursively corrected: 230
Number of output records: 82064 (94.05%)
Filter report:
Number of groups: 1253
Number of groups accepted: 958 (76.46%)
Total records weight: 82711.0
Records weight accepted: 82064.0 (99.22%)
Operator #0:
Effective threshold: 11.0
refineTagsAndSortrefineTagsAndSort{
"type": "refineTagsAndSort",
"commandLine": "--report results/01a_d110_LN_germCenterB.refine.report.txt --json-report results/01a_d110_LN_germCenterB.refine.report.json results/01a_d110_LN_germCenterB.vdjca results/01a_d110_LN_germCenterB.refined.vdjca",
"inputFiles": [
"results/01a_d110_LN_germCenterB.vdjca"
],
"outputFiles": [
"results/01a_d110_LN_germCenterB.refined.vdjca"
],
"version": "; built=Mon Sep 26 10:55:18 CEST 2022; rev=8c998df1ab; lib=repseqio.v2.0",
"correctionReport": {
"inputRecords": 87258,
"outputRecords": 82064,
"steps": [
{
"tagName": "UMI",
"inputGroups": 1,
"inputDiversity": 11117,
"inputCount": 87258,
"coreDiversity": 1852,
"coreCount": 77675,
"directlyCorrectedDiversity": 5364,
"directlyCorrectedCount": 5849,
"filteredDiversity": 4500,
"filteredCount": 4547,
"recursivelyCorrected": 230,
"diversityFilteredByWhitelist": 0,
"outputDiversity": 1253,
"outputCount": 82711
}
],
"filterReport": {
"type": "filter_groups_report",
"groupingKeys": [
"UMI"
],
"numberOfGroups": 1253,
"numberOfGroupsAccepted": 958,
"totalWeight": 82711,
"totalWeightAccepted": 82064,
"operatorReports": [
{
"type": "generic_hist_report",
"threshold": 11
}
],
"metricHists": [
{
"metric": {
"type": "group_metric_sum_weight",
"reportHist": {
"log": true,
"binNumber": 0,
"minBinWidth": 0.2
}
},
"hist": {
"bins": [
{
"from": 1,
"to": 1.5848931924611136,
"weight": 168
},
{
"from": 1.5848931924611136,
"to": 2.51188643150958,
"weight": 61
},
{
"from": 2.51188643150958,
"to": 3.981071705534973,
"weight": 13
},
{
"from": 3.981071705534973,
"to": 6.309573444801933,
"weight": 33
},
{
"from": 6.309573444801933,
"to": 10,
"weight": 19
},
{
"from": 10,
"to": 15.848931924611142,
"weight": 20
},
{
"from": 15.848931924611142,
"to": 25.11886431509581,
"weight": 45
},
{
"from": 25.11886431509581,
"to": 39.810717055349734,
"weight": 96
},
{
"from": 39.810717055349734,
"to": 63.09573444801933,
"weight": 199
},
{
"from": 63.09573444801933,
"to": 100,
"weight": 323
},
{
"from": 100,
"to": 158.48931924611142,
"weight": 170
},
{
"from": 158.48931924611142,
"to": 251.18864315095823,
"weight": 99
},
{
"from": 251.18864315095823,
"to": 398.1071705534973,
"weight": 7
}
],
"collectionSpec": {
"log": true,
"binNumber": 0,
"minBinWidth": 0.2
}
}
}
]
}
}
}
Correction Report
The following set of fields is reported for every processed tag-name. In this example the report only contains UMI tag.
UMI input diversity- Number of unique tag values in the input
vdjcafile. UMI output diversity- Number of unique tag values in the output
vdjcafile. UMI input reads- Total number of UMIs in the original
.vdjcafile (usually equals to the number of successfully aligned reads inmixcr alignreport) UMI output count- Total number of UMIs in the output file
UMI mean reads per tag- Average number of reads per UMI (equals
UMI input reads/UMI input diversity) UMI input core diversity- Number of UMIs used as a core.
UMI input core reads- Number of reads that contribute to core UMIs.
UMI directly corrected diversity- Number of unique UMI sequences that were corrected and assigned to the core UMIs (artificial diversity).
UMI directly corrected reads- Number of reads contributed to the corrected UMI sequences.
UMI diversity filtered by tag quality :
UMI reads filtered by tag quality :
UMI diversity filtered by whitelist- Number of unique UMIs left after whitelist filtering.
UMI recursively corrected
Number of output records :
Filter report
Number of groups- Initial number of unique groups of tags after correction.
Number of groups accepted- Number of unique groups of tags after filtering.
Total records weight- Total number of input groups.
Records weight accepted- Total number of groups of tags after filtering.
Effective threshold- Reads per group threshold used for filtering.