Low cell count #2082
Description
Checklist before submitting the issue:
- The issue is strongly related to the MiXCR software
- The issue can be reproduced with the most recent version of MiXCR
- There is no answer to the question in the official documentation and there is no duplicate issue in the bug tracker
- Inspection of raw alignments with exportAlignmentsPretty shows that data has the expected architecture, and sample preparation artefacts are not the reason of the problem (if this is the matter of the issue)
Expected Result
Thousands of cells in the output (tagValueCELL). My chemistry is "Single Cell 5' PE v3".
Actual Result
Only 18 cells.
Exact MiXCR commands
mixcr -Xmx48g analyze 10x-sc-xcr-vdj --species hsa ${FASTQ_R1} ${FASTQ_R2} sample_name
MiXCR report files
parse.report.txt
```
Execution time: 8.37m
Total reads: 154983195
Matched reads: 154983195 (100%)
Projection +R1 +R2: 154983195 (100%)
For variant 0:
For projection +R1 +R2:
CELL:Left position: 0
UMI:Left position: 16
CELL:Right position: 16
UMI:Right position: 26
R2:Left position: 0
Variants: 0
Cost: 0
CELL length: 16
UMI length: 10
R2 length: 150
```
refineTags.report.txt
```
Number of input records: 154983195
Number of output records: 75775 (0.05%)
CELL correction report:
CELL input diversity: 11719427
CELL output diversity: 2730 (0.02%)
CELL input records: 154983195
CELL output records: 76543 (0.05%)
CELL mean records per tag: 13.22
CELL input core diversity: 10767035 (91.87%)
CELL input core records: 154018909 (99.38%)
CELL directly corrected diversity: 1214999 (10.37%)
CELL directly corrected records: 2825120 (1.82%)
CELL diversity filtered by tag quality: 465037 (3.97%)
CELL records filtered by tag quality: 465411 (0.3%)
CELL diversity filtered by whitelist: 11251118 (96%)
CELL recursively corrected: 136651
UMI correction report:
UMI input groups: 2730
UMI input diversity: 26598
UMI output diversity: 25470 (95.76%)
UMI input records: 76543
UMI output records: 75775 (99%)
UMI mean records per tag: 2.88
UMI input core diversity: 25550 (96.06%)
UMI input core records: 75485 (98.62%)
UMI directly corrected diversity: 365 (1.37%)
UMI directly corrected records: 387 (0.51%)
UMI diversity filtered by tag quality: 763 (2.87%)
UMI records filtered by tag quality: 768 (1%)
UMI diversity filtered by whitelist: 0 (0%)
UMI recursively corrected: 3
```
I tried to change the tag pattern to --tag-pattern "^(CELL:N{16})(UMI:N{12})(R1:)^(R2:)" , but this didn't help.