extend report
MiXCR generates a comprehensive summary of extender performance. Extender reports may be generated right along with extend 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
============== Extend Report ==============
Input file(s): result/Treg_REH_4h_rep1.rescued_1.vdjca
Output file(s): result/Treg_REH_4h_rep1.extended.vdjca
Version: ; built=Fri Jul 15 01:51:38 CEST 2022; rev=aa769be87b; lib=repseqio.v2.0
Command line arguments: --report result/Treg_REH_4h_rep1.report --threads 24 result/Treg_REH_4h_rep1.rescued_1.vdjca result/Treg_REH_4h_rep1.extended.vdjca
Analysis time: 0ns
Extended alignments count: 152 (3.57%)
V extensions total: 0 (0%)
V extensions with merged targets: 0 (0%)
J extensions total: 152 (3.57%)
J extensions with merged targets: 0 (0%)
V+J extensions: 0 (0%)
Mean V extension length: NaN
Mean J extension length: 8.480263157894736
{
"type": "extenderReport",
"commandLine": "--report result/Treg_REH_4h_rep1.report --threads 24 result/Treg_REH_4h_rep1.rescued_1.vdjca result/Treg_REH_4h_rep1.extended.vdjca",
"inputFiles": [
"result/Treg_REH_4h_rep1.rescued_1.vdjca"
],
"outputFiles": [
"result/Treg_REH_4h_rep1.extended.vdjca"
],
"version": "; built=Fri Jul 15 01:51:38 CEST 2022; rev=aa769be87b; lib=repseqio.v2.0",
"totalProcessed": 4252,
"totalExtended": 152,
"vExtended": 0,
"vExtendedMerged": 0,
"jExtended": 152,
"jExtendedMerged": 0,
"vjExtended": 0,
"meanVExtensionLength": "NaN",
"meanJExtensionLength": 8.480263157894736
}
Extended alignments count- Number of extended alignments/clones
V extensions total- Number of V-gene extensions
V extensions with merged targets- Number of V-gene extensions that lead to the overlap of targets (e.g. R1 and R2)
J extensions total- Number of J-gene extensions
J extensions with merged targets- Number of J-gene extensions that lead to the overlap of targets (e.g. R1 and R2)
V+J extensions- Number of alignments/clones where both V and J genes were extended
Mean V extension length- Mean nucleotide length of V extensions
Mean J extension length- Mean nucleotide length of J extensions