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@aqzas @Huffyphenix ,
I am using CATT to extract TCR/BCR information from data from scRNA-seq of immune cells, involving more than 100 datasets. Your article gives a performance comparison of each to…
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Simultaneous analysis of several samples
Align individual samples:
```
mixcr align sample1_R1.fastq.gz sample1_R2.fastq.gz alignments1.vdjca
mixcr align sample2_R1.fastq.gz sample2_R2.fastq.gz…
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```
Exception in thread "main" java.lang.NegativeArraySizeException
at com.milaboratory.core.alignment.kaligner1.KMapper.align(KMapper.java:506)
at com.milaboratory.core.alignment.kaligner1.KAlig…
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Hi,
I previously used MiXCR4.1.2 align, assemble, etc. separately and get an alignment log like this:
```
Total sequencing reads: 11689853
Successfully aligned reads: 10588551 (90.58%)
...
```…
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This is a collection of issues that should be addressed during the next rework of `bripipetools`:
- [ ] add ATACseq #120 and Cut and Run functions
- [ ] push MiXCR data by project not flowcell #11…
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Hi. I have 10X genomic 5' scRNA-seq fastq files. I ran mixcr like so:
~/mixcr analyze 10x-5gex-full-length --species hsa $sample\_R1_001.fastq.gz $sample\_R2_001.fastq.gz $output/$sample
I exporte…
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- [ ] Review by BS
- [x] Tessa etc output in multimodal integration way way too verbose. Silence it
- [ ] Update https://www.sc-best-practices.org/air_repertoire/ir_profiling.html#immune-receptor-se…
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Hi Dr. Nazarov
I found another bug, may not a bug? Could please help check? When I use the top() function, I set ".n" = 50, however, in some sample, I can get more rows than 50, in fact, in your da…
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## Summary
We need a minimum of 30x coverage in order to confidently identify unique VDJ sequences as truly unique. In addition, we need to ensure that this coverage amount can be met for all samples…
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We use multiplex PCR +gDNA to amplify human IGK with V and JK-KDE primers.
After we assembled clones we almost got no clone reads.
> IGK chains: 706756 (99.94%)
but,
> Reads dropped due to …