Are there exporting parameter for filtering the tree with only paired light and heavy chain for scBCR-seq data

[Jianche666]

Checklist before submitting the issue:

• [yes] The issue is strongly related to the MiXCR software
• [yes] The issue can be reproduced with the most recent version of MiXCR
• [yes] There is no answer to the question in the official documentation and there is no duplicate issue in the bug tracker

I am using the mixcr exportShmTreesWithNodes sample1.shmt sample1_tree1.tsv to analyze my scBCR-seq data.

This is the original log from mixcr. I only want to keep the trees with only paired lights and heavy chains (IGH + IGL or IGH + IGK). I wonder if there is filtering parameter I can add to the function as I noticed mixcr definitely stored the information in the project from the code log.

Group clones by the same V, J and CDR3Length: 0%
Step 1/3, Building initial trees: 0%
Step 2/3, Attaching clones by distance change: 0%
Step 3/3, Combining trees: 0%
Group trees by cells: 0%
Writing results 2/2: 0%
Writing clones: 0%
=================== report: findShmTrees ===================
Analysis time: 5.47s
Step 1: Building initial trees
  Clones was added: 335
  Trees created: 126
Step 2: Attaching clones by distance change
  Clones was added: 7
Step 3: Combining trees
  Trees combined: 5
Trees count before combination by cells: 121
Trees count after combination by cells: 97 (80.17%)
Clones count before combination by cells: 342
Clones count after combination by cells: 97 (28.36%)
Secondary chains split by difference in CDR3: 0
Sub trees combined because of similar NDN: 0
Counts of secondary chains before combination:
1: 24 (28.57%)
2: 38 (45.24%)
3: 14 (16.67%)
4: 4 (4.76%)
21: 1 (1.19%)
5: 2 (2.38%)
7: 1 (1.19%)
Secondary chains combined in one tree because of broad overlap:
2: 18
3: 3
Clone groups with contradictions with main chain: 19
Clone groups not used as links because its clones ended up in the same tree: 3
Clone groups with invalid chains: 10
Filtered out subtrees with only one node: 12
Trees with several chains: 85 (87.63%)
Trees with incompatible chains: 0 (0%)
Trees with more than two chains of the same type: 5 (5.88%)
Number of trees per type:
1 IGH, 1 IGK: 34 (40%)
1 IGH, 1 IGL: 18 (21.18%)
2 IGH, 1 IGK: 8 (9.41%)
1 IGH, 2 IGL: 5 (5.88%)
2 IGH, 1 IGL: 3 (3.53%)
2 IGH, 2 IGK: 3 (3.53%)
2 IGH, 2 IGL: 3 (3.53%)
3 IGH, 1 IGK: 3 (3.53%)
1 IGH, 2 IGK: 2 (2.35%)
       2 IGH: 2 (2.35%)
       2 IGK: 1 (1.18%)
       2 IGL: 1 (1.18%)
1 IGH, 3 IGK: 1 (1.18%)
3 IGH, 1 IGL: 1 (1.18%)
Clones count in trees per type:
1 IGH, 1 IGK: 134 (30.88%)
1 IGH, 1 IGL: 75 (17.28%)
1 IGH, 3 IGK: 53 (12.21%)
2 IGH, 1 IGK: 33 (7.6%)
1 IGH, 2 IGL: 30 (6.91%)
2 IGH, 1 IGL: 21 (4.84%)
3 IGH, 1 IGK: 19 (4.38%)
2 IGH, 2 IGL: 18 (4.15%)
2 IGH, 2 IGK: 16 (3.69%)
1 IGH, 2 IGK: 12 (2.76%)
       2 IGH: 8 (1.84%)
       2 IGK: 6 (1.38%)
3 IGH, 1 IGL: 6 (1.38%)
       2 IGL: 3 (0.69%)
Clones in trees with only one chain: 26 (7.6%)
Trees with only one chain: 12 (12.37%)
Total trees count: 97
Total clones count in trees: 460 ````


Thank you!

[mizraelson]

Hi, there is no filter for that, as within a single tree some clones may have both chains present in the data, while for others the second chain would be reconstructed.

[lejecrs]

Hi would it be possible for a complete tutorial on the single-cell BCR analysis tutorial, or the feature of what's new you can do with scBCR compared to bulk in MiXCR.