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What data format do you have in example/COVID/COVID_1.zip? How do I get from my MIXCR output into a format suitable for fastBCR?
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Hi,
I'm using scRepertoire v 2.0.0 and the `combineTCR()`. With this package version there are the gene columns "v_gene", "d_gene" and "j_gene" and the "chain" column. However, I think there should…
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## 🐛 Bug
Hi, I keep getting an error trying to load any MiXCR output to Immunarch. The message "Samples found in the metadata, but not in the folder" is not helpful, but the issue I think is that I…
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Hi @ncborcherding thank you so much for developing scRepertoire this is a really great tool!
Soon I'll be working with BCR + scRNA data and I would like to use MiXCR for the analysis of clones tree…
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Hello,
I had a question regarding the MiXCR's defaut library reference sequences. I noticed there were some differences in terms of list of alleles for specific v genes and what v genes were inclu…
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## Checklist before submitting the issue:
- [x] The issue is strongly related to the MiXCR software
- [x] The issue can be reproduced with [the most recent version](https://github.com/milaborato…
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Hello ncborcherding,
I tried to use `Euclidean distance` to compare samples.
Thank you in advance for your great help!
Best,
Yue
```
combined.TCR
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I've tried to use my ONT data (I used SQK-LSK109 kit for IGHV sequencing) to analyze data but alignment stops at some point and I don't understand whats wrong?
'mixcr align --report CLL-0895_result…
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## 🐛 Bug
Hi!
The tutorial suggests various file types can be loaded, with various names, as long as the basename is in the metadata table. Meanwhile, I resorted to AIRR because MiXCR files seemed…
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I am running MiXCR with
tag_pattern='^(UMI:N{12})(R1:*)\(R2:*)'
java -Xmx16g -jar $mixcr analyze generic-amplicon-with-umi \
--species hsa \
--assemble-clonotypes-by CDR3 \
…