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When I run commandline with "mixcr exportPlots shmTrees --metadata /home/EXP0033VH/metadata.tsv --node-color sample --line-color sample --node-label sample --alignment-aa CDR3 /home/EXP0033VH/findal…
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Hi developer,
We always run into the issue of "cannot execute binary file", and I think it might be related to **mixcr licensce**. I have obtained the licensce, how do I provide it to the pipeline…
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Dear Phil,
After reading your paper I would be interested in checking identifying shared motifs in a particular subset of sorted T cells that undergo strong TCR signaling during their development in …
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## Summary
MiXCR performs an alignment as well as an assembly step during its process of identifying clonotypes. During assembly, a clustering method is utilized to attempt to overcome PCR and sequen…
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Hi,
We recently ran TRUST4 on some 10x Genomics TCR data using the command
`trust4 -f hg38_bcrtcr.fa --ref human_IMGT+C.fa -1 input/YWI006-VDJ_S1_L001_R1_001.fastq.gz -2 input/VDJ/YWI006-VDJ_S1_L001…
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Hello, thank you very much for providing the RTCR code. It helps with replacing mixcr for analysis.
However, I have noticed two issues:
I noticed that the nucleotide sequences for CDR3 in RTCR an…
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Hello again! This is a follow-up to issue #247, thank you so much for your insights there!
So I managed to run TRUST4 on my SMARTer data with the following command (which still took really too long…
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Hi Quentin,
Can IGoR process paired end sequences? I didn't see this option in the manual input file section, see below,
_Can be a fasta file, a csv file (with the sequence index as first column…
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Dear Dr. Li,
Firstly, I would like to express my gratitude for creating such excellent tools.
I have utilized TRUST4 to analyze my different spatial TCR data set (TRA and TRB are enriched separ…
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### Overview
While working on issue #11, mixcr began to throw an error while trying to maintain read IDs during the align and assembly process. We need to include the read ids in our pipeline so that…