Tag: mixcr

Forum:Is there a way to run MiXCR with fasta sequences 0 I’m trying to perform B cell sequence alignment (VH region) using MiXCR, but according to the documentation I’ve read, it requires raw fastq.gz reads. I attempted to use fasta sequences instead of raw fastq, but I encountered an error:…

About MiXCR As a rapidly growing startup at the forefront of biotechnology, we are pioneering the advancement of software solutions for the analysis of Next-Generation Sequencing (NGS) data in Immune Profiling. Our flagship product, MiXCR, is being leveraged by thousands of academic researchers worldwide, government agencies, and innovative biopharmaceutical and…

POSITION SUMMARY: We are seeking an immunologist with bioinformatics experience to join a multidisciplinary team developing leading-edge genomics analysis tools to understand the immune system’s response to cancer. This highly motivated, detail-oriented individual would join a clinical genomics analysis group and will be responsible for developing and applying bioinformatics methods…

BCR/TCR analysis using target capture sequencing data 0 Hi all, MIXCR is widely used to analyze the TCR/BCR sequencing data, which usually use the multiplex amplicon sequencing method. We have design the 120bp probe to capture all the genes across IGH/IGL/IGK and TCR locus. Since the latest mixcr v4 used…

Introduction Cholangiocarcinoma (CC) is a form of gastrointestinal cancer that originates from the epithelium of either intrahepatic or extrahepatic bile ducts. It accounts for approximately 3% of all gastrointestinal cancers, with reported incidence of one to two cases per 100,000 persons per year in the USA (and much higher incidence…

how to identify CDR region in antibody sequence 2 I want to extract CDR region form an antibody sequence or numbered antibody sequence. Because SCALOP will miss H-CDR3, is there annother tool could identify CDR region? After numbering the antibody sequence by ANARCI, whether it’s the right way to extract…

Schumacher, T. N. & Schreiber, R. D. Neoantigens in cancer immunotherapy. Science 348, 69–74 (2015). Article  ADS  CAS  PubMed  Google Scholar  Tran, E., Robbins, P. F. & Rosenberg, S. A. Final common pathway’ of human cancer immunotherapy: targeting random somatic mutations. Nat. Immunol. 18, 255–262 (2017). Article  CAS  PubMed  PubMed…

Normalizing TCR data 1 Hi, What’s the best method to normalize TCR repertoire data (for comparison between samples) which already has raw counts and count frequency. Already tried Counts per Million (CPM) but there’s a possibility that it might exaggerate the count number of a clone so the real picture…

Redirect output from MIXCR 2 If your command is: mixcr analyze amplicon -s <species> \ –starting-material <startingmaterial> \ –5-end <5End> –3-end <3End> \ –adapters <adapters> \ [OPTIONS] input_file1 [input_file2] analysis_name then set analysis_name as path/to/analysis/analysis_name Just add the path as a part of the prefix for output files: e.g. mixcr…

Track Clonotypes with TCR Sequence on standard Single Cell data (not scTCR-Seq) 1 Hello, I used MIXCR on standard Single Cell data and found some common clonotypes among my multiple conditions. I would like to know if it would be possible to track clonotypes with the TCR Sequence ? If…

Nextseq and Miseq data output difference? 2 Hi, Is it ok to run a Mixcr pipeline on a TCR sequencing dataset, half of which was processed on Nextseq and half on Miseq? What is the major difference among Nextseq and Miseq platforms? Thanks, Payal sequencing • 2.0k views • link…

Comparing 5’RACE TCR Sequencing Methods 1 Hello, My laboratory developed an in-house 5’RACE method with custom primers targeting the constant region of the gamma/delta T cells. We submitted RNA to a third party commercial laboratory to benchmark our method against their 5’RACE method. Both our in-house fastq’s and the third…

Detection T cell receptor transcripts 2 Hello, I planned to explore diverse T cell receptor transcripts using long-read sequencing. So I transfected TCR mini gene into cells and got sequencing data. I mapped my data to genome reference and visualize it via IGV. But I couldn’t see any transcripts from…

filter out T cell clones 2 Dear all, I just mapped some bulk Seq reads to reference VDJ genes of T cell receptors in order to extract the T cell clonotypes (using mixcr). The resulted clonotypes come in a txt file per sample that looks like this: count freq cdr3nt…

If you have non-enriched (I mean non-V(D)J-enriched, after emulsion) 5′ single-cell 10x data, prepared according to the 10x’s manual, then, very approximately, you should catch 30~50% of the T-cells, with 20~30% of the cells having both TRA+TRB chains (the main factor here seems to be the quality of size selection,…

TCR data analysis 1 We are using Takara a/b TCR profiling kit. The libraries were run on MiSeq 600 and we got 600,000 to 1400,000 reads per sample. Before analysis using MIXCR, should the reads be downsampled? Should negative and positive controls be included in the analysis? What are the…

Low alignment rates for randomly shredded TCR-B library with MixCR 1 Hello community, Apologies for cross-posting my query here along with the github page for MixCR. I am hoping to seek help from a wider community here. I recently applied the MiXCR pipeline in ‘shotgun’ mode to analyze my randomly…

MiXCR error with the complied cat TCR library 0 Dear great helpers, I compiled json library for cat’s TCR using ‘repseqio’ as attached file. The command lines were as followed: $MIXCR analyze amplicon –threads 20 –library imgt –species “cat” –starting-material rna –5-end v-primers –3-end j-primers –adapters adapters-present –receptor-type tcr –region-of-interest…