We use cookies to improve your browsing experience and provide meaningful content. Read our cookie policy. Accept
  •  Customer Login
  • Register
  •  View Cart (0)
  •  Customer Login
  • Register
  •  View Cart (0)

  • Products
  • Services & Support
  • Learning centers
  • APPLICATIONS
  • About
  • Contact Us

Close

  • ‹ Back to Cogent NGS Immune Profiler
  • Cogent NGS Immune Profiler Software notices
  • Cogent NGS Immune Profiler Software videos
Software for BCR/TCR sequencing analysis Cogent NGS Immune Profiler software tool
NGS product page SMART-Seq Human BCR (with UMIs) product page
SMARTer TCRv2 kit product page Human TCRv2 profiling kit product page
Home › Learning centers › Next-generation sequencing › Bioinformatics resources › Cogent NGS Immune Profiler › Cogent NGS Immune Profiler Software notices

Bioinformatics resources

  • Cogent NGS Analysis Pipeline
    • Cogent NGS Analysis Pipeline notices
  • Cogent NGS Discovery Software
    • Cogent NGS Discovery Software notices
  • Cogent NGS Immune Profiler
    • Cogent NGS Immune Profiler Software notices
    • Cogent NGS Immune Profiler Software videos
  • Cogent NGS Immune Viewer
  • Embgenix Analysis Software
  • ICELL8 scTCR Analyzer
  • SMARTer Human scTCR Demultiplexer
  • SMART-Seq DE3 Demultiplexer
New products
Need help?
Contact Sales
Software for BCR/TCR sequencing analysis Cogent NGS Immune Profiler software tool
NGS product page SMART-Seq Human BCR (with UMIs) product page
SMARTer TCRv2 kit product page Human TCRv2 profiling kit product page

Cogent NGS Immune Profiler Software notices

The issues described below for the Cogent NGS Immune Profiler Software are ones that have been seen or reported. If you encounter other errors using Immune Profiler or are unable to resolve the problem using the suggestions below, please:

  1. Capture a screenshot of the text of the error you see on the screen.
  2. Gather the relevant log file(s). Refer to the FAQ entry below or the Cogent NGS Immune Profiler User Manual, Appendix B, for more detailed information about the logs.
  3. Send the screenshot and gathered log file(s) to Technical Support along with a brief description of the issue.

Software issues FAQs

Common error messages on Linux

SyntaxError: invalid syntax

Problem description

If calling the script at the command line in the format of python immune_profiler.py [variables], a message "SyntaxError: invalid syntax" is seen.

Cause

Python2 is the default version on the machine.

Fix

Use the syntax: python3 immune_profiler.py [variables]

immune_profiler.py: error: the following arguments are required

Problem description

The immune_profiler.py script is returning the message similar to the following:

"immune_profiler.py: error: the following arguments are required: [variables]"

Cause

Immune Profiler has five required arguments:

Flag Parameter input
-f fastq_dir
-m meta_file
-o output_name
-r receptor_type
-t target_region

If any of the required argument is missing, this error is seen indicating which argument is missing.

Fix

Make sure to specify all five required arguments for the script command. Please see the Quick Start Guide or User Manual if more information is needed.

IndexError: list index out of range

Problem description

The immune_profiler.py script is returning the message:

"IndexError: list index out of range"

Cause

This error might be seen if the argument value of the -o parameter is given in a path structure + output name string.  The output name specified by -o is supposed to be an alphanumeric string with no special characters other than hyphens.

Fix

Modify the value of the -o parameter to be only a string with no directory path in it.

[ERROR] Found duplicate sample ID

Problem description

The immune_profiler.py script is returning the message:

"[ERROR] Found duplicate sample ID: [variable]"

Cause

A duplicate sample ID value was detected in the metadata file.

Fix

Use the ID value stated in the error message to identify the duplicate in the metadata CSV file and update it to a value that would not duplicate any other values in the file.

[ERROR] Found _ in sample ID

Problem description

The immune_profiler.py script is returning the message: 

"[ERROR] Found _ in sample ID: [variable]"

Cause

A sample ID in the metadata CSV file was found to include an underscore character (_).

Fix

Edit the metadata file to change the sample ID name to remove the underscore. Valid characters include alphanumerics or hyphens, no other special characters.

[WARN] Delete empty sample ID in meta file

Problem description

The immune_profiler.py script is returning the message:

"[WARN] Delete empty sample ID in meta file: [variable]"

Cause

The script found one or more empty lines in the metadata CSV file.

Fix

No action is required; this is a warning message only. The script will, in addition to the warning, also delete the empty line from the file and report on the actual number of samples to process (non-empty rows).

[ERROR] The input FASTQ: [filename] is not found.

Problem description

The immune_profiler.py script is returning the message:

"[ERROR] The input FASTQ: [filename] is not found."

Cause

The FASTQ file name(s) configured in the metadata CSV file do not match or do not exist in the directory specified by the path parameter of the -f flag of the script.

Fix

  1. If the path statement to the FASTQ files is incorrect in the script command, correct the path value.
  2. Check the name of the FASTQ file(s) listed in the metadata file, and update the FASTQ file name(s) to exactly match between the metadata file configuration and the actual file name.

Common error messages on MacOSX

[Error] Parameter definition not found/needs to be defined/selected

Problem description

The user interface status screen is showing the message:

"Finished
An error has occurred."

and one or more of the following explanations:

  • "[Error] The fastq directory is not found"
  • "[Error] The metadata file is not found"
  • "[ERROR] Please define output name"
  • "[ERROR] Please select receptor type"
  • "[ERROR] Please select target region"

Cause

Immune profiler has five required arguments:

  1. FASTQ directory
  2. Metafile location
  3. Output name
  4. Receptor type
  5. Target region

These messages may be seen if any of the required fields are not configured in the user interface.

Fix

Make sure to configure all five required arguments on the input fields screen. Please see the Quick Start Guide or User Manual if more information is needed.

[ERROR] Found duplicate sample ID

Problem description

The user interface status screen is showing the message:

"[ERROR] Found duplicate sample ID: [variable]
[INFO] Immune profiler analysis ends with error"

Cause

A duplicate sample ID value was detected in the metadata file.

Fix

Use the ID value stated in the error message to identify the duplicate in the metadata CSV file, and update it to a value that would not duplicate any other values in the file.

[ERROR] Found _ in sample ID

Problem description

The user interface status screen is showing the message:

"[ERROR] Found _ in sample ID: [variable]
[INFO] Immune profiler analysis ends with error"

Cause

A sample ID in the metadata CSV file was found to include an underscore character (_).

Fix

Edit the metadata file to change the sample ID name to remove the underscore. Valid characters include alphanumerics or hyphens, no other special characters.

[WARN] Delete empty sample ID in meta file

Problem description

The user interface status screen is showing the message:

"[WARN] Delete empty sample ID in meta file: [variable]
[WARN] After deletion, ## samples to process
[WARN] Please check and modify meta file if the sample number is incorrect
[WARN] Check if there is any extra empty line in meta file"

Cause

Profiler found one or more empty lines in the metadata CSV file.

Fix

No action is required; this is a warning message only. The program will, in addition to the warning, also delete the empty line from the file and report on the actual number of samples to process (non-empty rows).

[ERROR] The input FASTQ: [filename] is not found.

Problem description

The user interface status screen is showing the message:

"[ERROR] The input FASTQ: [filename] is not found.
Please make sure the FASTQ directory & FASTQ name in metadata file is correct (case sensitive)
Immune profiler error
[INFO] Immune profiler analysis ends with error"

Cause

The specified FASTQ file name(s) configured in the metadata CSV file do not match or do not exist in the directory specified in the required arguments configuration screen.

Fix

  1. If the path statement to the FASTQ files is incorrect in the script command, correct the path value.
  2. Check the name of the FASTQ file(s) listed in the metadata file, and update the FASTQ file name(s) to exactly match between the metadata file configuration and the actual file name.

List & description of log files

The table contains the log filename, the location where to find them within the immune_profiler/ directory, and a brief description of the information stored in each. This information is also documented in the Cogent NGS Immune Profiler User Manual.

The string [cdr3|fl] means either CDR3 or Full_length. E.g., run_mixcr_fl.log

Log filename Sub-folder Description
_immune_profiler.log -- Immune Profiler analysis progress and important notes
mig_run_migec.log run_migec/ MIGEC analysis progress
mig_run_migec.error run_migec/ MIGEC error messages (if any)
assemble.log.txt run_migec/assemble MIGEC process status
assemble.cmd.txt run_migec/assemble The command call to MIGEC for the assemble function
checkout.cmd.txt run_migec/ checkout_all/ MIGEC analysis commands used
checkout.log.txt run_migec/ checkout_all/ MIGEC analysis progress and findings
checkout.filelist.txt run_migec/ checkout_all/ Documents all intermediate files while MIGEC is processing
run_mixcr_[cdr3|fl].log run_mixcr/ MIXCR analysis progress and important notes
NOTE: Different files are created depending on whether the CDR3 or full-length target regions are selected during configuration
run_mixcr_[cdr3|fl].error run_mixcr/ MIXCR error messages (if any)
NOTE: Different files are created depending on whether the CDR3 or full-length target regions are selected during configuration

Data analysis FAQs

Examples of BCR output from Immune Profiler

Example: Ig libraries share the same index

If only one index is used, only one pair of Read 1 and Read 2 FASTQ (*.fastq.gz) files will be generated by demultiplexing, for instance: S1_R1.fastq and S1_R2.fastq.

Immune Profiler divides the reads into four classes—IgG, IgM, IgK, and IgL—based on their sequences and makes clonotype calls. The summary report will resemble:

Sample type Total reads Total MIG UMI threshold Number of reads after MIG collapse Aligned Pair‑read overlap Overlapped and aligned Clonotype count
S1_IGG 93,710 6,422 16 366 265 326 259 132
S1_IGM 94,200 8,528 8 949 821 831 753 448
S1_IGK 93,813 9,543 6 1,949 1,884 1,905 1,881 1,054
S1_IGL 91,691 8,512 6 1,680 1,603 1,640 1,563 883

Table 1. Example Immune Profiler report spreadsheet output when a single index is used.

Example: Ig libraries have different indexes

If the libraries are labelled with multiple indexes, more than one pair of FASTQ (*.fastq.gz) files will be generated after demultiplexing, for example: S1_IgG_R1.fastq and S1_IgG_R2.fastq, S1_IgM_R1.fastq and S1_IgM_R2.fastq, etc.

Immune Profiler divides the reads into the four classes: IgG, IgK, IgL, and IgM. The summary report will resemble:

Sample type Total reads Total MIG UMI threshold Number of reads after MIG collapse Aligned Pair-read overlap Overlapped and aligned Clonotype count
S1‑G_IGG 93,678 6,413 16 366 265 326 259 132
S1‑G_IGM 13 7 1 7 7 4 4 2
S1‑G_IGK 7 2 1 2 2 2 2 0
S1‑G_IGL 12 9 1 9 9 8 8 2
S1‑M_IGG 7 3 1 3 3 3 3 0
S1‑M_IGM 94,155 8,506 8 949 821 830 752 448
S1‑M_IGK 6 5 1 5 5 5 5 2
S1‑M_IGL 12 10 1 10 10 10 10 2
S1‑K_IGG 17 11 1 11 8 7 6 1
S1‑K_IGM 18 12 1 12 10 8 8 1
S1‑K_IGK 93,792 9,536 6 1,949 1,884 1,905 1,881 1,054
S1‑K_IGL 25 14 1 14 14 12 12 4
S1‑L_IGG 8 6 1 6 5 3 3 1
S1‑L_IGM 14 6 1 6 5 3 2 0
S1‑L_IGK 8 3 1 3 3 3 3 1
S1‑L_IGL 91,642 8,497 6 1,680 1,603 1,640 1,563 883

Table 2. Example Immune Profiler report spreadsheet output when multiple (four) indexes are used

In the table, all four indexes (IgG, IgM, IgK, and IgL) are used. Each Ig sample type (e.g., S1-G, representing an IgG sample) has a row tagged with each index.

It is expected that a small number of total reads (usually <0.05%) are miscategorized and incorrectly identified on the report due to cross-contamination from the library preparation process or index hopping during sequencing. In each of the above cases, the predominant clonotype reported in the sample matches the index (i.e., S1-G and IgG, S1-K and IgK, etc.).

How to determine if BCR input data is of low sequencing quality

Example: good sequencing data

In this sequencing run, we loaded a pool of IgM and IgL libraries, from 1,000 ng PBMC RNA input at ~10 million reads per library, on the same flow cell.

As shown in the QC stats table, IgM is the main chain identified in Sample_ID 1000ng-IgM, and IgL is the main chain identified in 1000ng-IgL. The other chains read in the sample are less than 0.1% of the total reads, indicating that index hopping and cross-contamination from library preparation of IgG, IgK, and the nondominant Ig type for the sample (IgL for the IgM sample, IgM for the IgL sample) are below an acceptable level.

Sample_ID IGG IGM IGK IGL Short Undetermined flc Total
1000ng‑IgM 0
(0.0%)
8,530,650
(94.8%)
10
(0.0%)
1,982
(0.0%)
0
(0.0%)
116,026
(1.3%)
351,332
(3.9%)
9,000,000
(100.0%)
1000ng‑IgL 38 (0.0%) 1,895 (0.0%) 15 (0.0%) 8,456,630 (94.0%) 0 (0.0%) 192,472 (2.1%) 348,950 (3.9%) 9,000,000 (100.0%)

Table 3. Example from sample_QC_stats.csv displaying the results of good sequencing data.

In the mapping_stats.csv report, we notice that the “total reads” are roughly equivalent when compared to the value in the sample_QC stats.csv.

Sample type Total reads Total MIG UMI threshold Number of reads after MIG collapse Aligned Pair‑read overlap Overlapped and aligned Clonotype count
1000ng‑IgM_IGM 8,530,650 444,674 6 122,399 103,787 105,836 93,609 53,063
1000ng‑IgM_IGK 10 2 1 2 1 2 1 0
1000ng‑IgM_IGL 1,982 926 1 926 865 711 661 62
1000ng‑IgL_IGG 38 22 1 22 22 18 18 3
1000ng‑IgL_IGM 1,895 615 1 615 480 273 202 40
1000ng‑IgL_IGK 15 8 1 8 3 2 2 1
1000ng‑IgL_IGL 8,456,630 669,152 4 275,140 262,494 271,499 259,397 29,335

Table 4. Example from mapping_stats.csv reads displaying the results of good sequencing data.

Example #1:
1000ng-IgM
sample_QC_stats.csv reads: 8,530,650
mapping_stats.csv reads: 8,530,650

Example #2:
1000ng-IgK
sample_QC_stats.csv reads: 8,456,630
mapping_stats.csv reads: 8,456,630

The equivalency of total reads between the two files indicates that few or no reads were discarded during the threshold check by MIGEC during processing and that MIGEC has determined that the input sequencing data is of good quality.

Example: poor sequencing data

In the sequencing results shown below, we loaded a pool of IgG and IgK libraries, from 1,000 ng PBMC RNA input at ~10 million reads per library, on the same flow cell.

As shown in QC stats table, IgG is the main chain identified in Sample_ID 1000ng-IGG, and IgK is the main chain identified in 1000ng-IGK.

Sample_ID IGG IGK IGL IGM Short Undetermined flc Total
1000ng‑IGG 9,443,333
(94.4%)
708
(0.0%)
104
(0.0%)
0
(0.0%)
0
(0.0%)
204,032
(2.0%)
351,823
(3.5%)
10,000,000
(100.0%)
1000ng‑IGK 5,197
(0.1%)
8,973,560
(94.7%)
1
(0.0%)
2
(0.0%)
0
(0.0%)
167,327
(1.8%)
326,252
(3.4%)
9,472,339
(100.0%)

Table 5. Example from sample_QC_stats.csv displaying the results of using poor-quality sequencing data.

In the mapping_stats.csv report, we notice that the "total reads" dropped significantly compared to the value in the sample_QC stats.csv.

Sample type Total reads Total MIG UMI threshold Number of reads after MIG collapse Aligned Pair‑read overlap Overlapped and aligned Clonotype count
1000ng‑IGG_IGG 4,844,692 247,936 6 74,221 66,623 68,411 63,275 5,884
1000ng‑IGG_IGK 403 251 1 251 245 114 109 1
1000ng‑IGG_IGL 41 21 1 21 15 6 4 1
1000ng‑IGK_IGG 3,219 2,018 1 2,018 1,859 472 396 10
1000ng‑IGK_IGM 2 2 1 2 2 2 2 1
1000ng‑IGK_IGK 4,618,169 655,183 3 365,885 354,951 360,270 353,187 30,486
1000ng‑IGK_IGL 0 0 1 0 0 0 0 0

Table 6. Example from mapping_stats.csv reads displaying the results of using poor-quality sequencing data.

Example #3:
1000ng-IGG
sample_QC_stats.csv reads: 9,443,333
mapping_stats.csv reads: 4,844,692

Example #4:
1000ng-IGKs
sample_QC_stats.csv reads: 8,973,560
mapping_stats.csv reads: 4,618,169

This discrepancy in total reads between the two reports is due to MIGEC excluding reads based on the calculated exclusion threshold. The quality of the UMI region is determined to be poor, so the reads are not processed or reported in the mapping stats report.


Profiling human B-cell receptors with SMART technology

Analyze BCR repertoires from human PBMCs or purified B cells.

Human TCRv2 profiling kit for Illumina sequencing

SMARTer TCR profiling with optimized chemistry, UMIs, UDIs, and bioinformatics support for more accurate, reliable clonotype calling and quantification.

Cogent NGS Immune Profiler Software

Analyze sequence data prepared using our BCR or TCR profiling kits.

Takara Bio USA, Inc.
United States/Canada: +1.800.662.2566 • Asia Pacific: +1.650.919.7300 • Europe: +33.(0)1.3904.6880 • Japan: +81.(0)77.565.6999
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES. © 2022 Takara Bio Inc. All Rights Reserved. All trademarks are the property of Takara Bio Inc. or its affiliate(s) in the U.S. and/or other countries or their respective owners. Certain trademarks may not be registered in all jurisdictions. Additional product, intellectual property, and restricted use information is available at takarabio.com.

Takara Bio USA, Inc. provides kits, reagents, instruments, and services that help researchers explore questions about gene discovery, regulation, and function. As a member of the Takara Bio Group, TBUSA is part of a company that holds a leadership position in the global market and is committed to improving the human condition through biotechnology. Our mission is to develop high-quality innovative tools and services to accelerate discovery.

FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES (EXCEPT AS SPECIFICALLY NOTED).

Support
  • Contact us
  • Technical support
  • Customer service
  • Shipping & delivery
  • Sales
  • Feedback
Products
  • New products
  • Special offers
  • Instrument & reagent services
Learning centers
  • NGS
  • Gene function
  • Stem cell research
  • Protein research
  • PCR
  • Cloning
  • Nucleic acid purification
About
  • Our brands
  • Careers
  • Events
  • Blog
  • Need help?
  • Announcements
  • Quality and compliance
  • That's Good Science!
Facebook Twitter  LinkedIn

©2023 Takara Bio Inc. All Rights Reserved.

Region - North America Privacy Policy Terms and Conditions Terms of Use

Top



  • COVID-19 research
  • Viral detection with qPCR
  • SARS-CoV-2 pseudovirus
  • Human ACE2 stable cell line
  • Viral RNA isolation
  • Viral and host sequencing
  • Vaccine development
  • CRISPR screening
  • Drug discovery
  • Immune profiling
  • Publications
  • Next-generation sequencing
  • RNA-seq
  • DNA-seq
  • Single-cell NGS automation
  • Reproductive health
  • Bioinformatics tools
  • Whole genome amplification
  • Immune profiling
  • Diagnostic solutions
  • Reproductive health
  • Real-time PCR
  • Real-time PCR kits
  • Reverse transcription prior to qPCR
  • High-throughput qPCR solutions
  • RNA extraction and analysis for real-time qPCR
  • Stem cell research
  • Media and supplements
  • Stem cells and stem cell-derived cells
  • Single-cell cloning of edited hiPS cells
  • mRNA and cDNA synthesis
  • In vitro transcription
  • cDNA synthesis kits
  • Reverse transcriptases
  • RACE kits
  • Purified cDNA & genomic DNA
  • Purified total RNA and mRNA
  • PCR
  • Most popular polymerases
  • High-yield PCR
  • High-fidelity PCR
  • GC rich PCR
  • PCR master mixes
  • Cloning
  • In-Fusion seamless cloning
  • Competent cells
  • Ligation kits
  • Restriction enzymes
  • Nucleic acid purification
  • Plasmid purification kits
  • Genomic DNA purification kits
  • DNA cleanup kits
  • RNA purification kits
  • Cell-free DNA purification kits
  • Microbiome
  • Gene function
  • Gene editing
  • Viral transduction
  • Fluorescent proteins
  • T-cell transduction and culture
  • Tet-inducible expression systems
  • Transfection reagents
  • Cell biology assays
  • Protein research
  • Purification products
  • Two-hybrid and one-hybrid systems
  • Mass spectrometry reagents
  • Antibodies and ELISAs
  • Primary antibodies and ELISAs by research area
  • Fluorescent protein antibodies
  • New products
  • Special offers
  • Baculovirus titration kits early access program
  • NGS bundle and save
  • TALON his-tag purification resin special offer
  • GoStix Plus special offers
  • PCR samples
  • Instrument services
  • Apollo services
  • ICELL8 services
  • SmartChip services
  • OEM & custom enzyme manufacturing
  • Services
  • Quality
  • Expertise
  • OEM enzyme FAQs
  • Custom enzyme samples
  • Exploring OEM and custom enzyme partnerships
  • Stem cell services
  • Clinical-grade stem cell services
  • Research-grade stem cell services
  • Outsourcing stem cell-based disease model development
  • Gene and cell therapy manufacturing services
  • Services
  • Facilities
  • Our process
  • Resources
  • Customer service
  • Sales
  • Make an appointment with your sales rep
  • Shipping & delivery
  • Technical support
  • Feedback
  • Online tools
  • GoStix Plus FAQs
  • Partnering & Licensing
  • Vector information
  • Vector document overview
  • Vector document finder
Takara Bio's award-winning GMP-compliant manufacturing facility in Kusatsu, Shiga, Japan.

Partner with Takara Bio!

Takara Bio is proud to offer GMP-grade manufacturing capabilities at our award-winning facility in Kusatsu, Shiga, Japan.

  • Automation systems
  • SmartChip Real-Time PCR System introduction
  • ICELL8 introduction
  • Next-generation sequencing
  • Technical notes
  • Featured kits
  • Technology and application overviews
  • FAQs and tips
  • DNA-seq protocols
  • Bioinformatics resources
  • Webinars
  • cDNA synthesis
  • Real-time PCR
  • Overview
  • Reaction size guidelines
  • Guest webinar: extraction-free SARS-CoV-2 detection
  • Guest webinar: developing and validating molecular diagnostic tests
  • Technical notes
  • Nucleic acid purification
  • Nucleic acid extraction webinars
  • Product demonstration videos
  • Product finder
  • Plasmid kit selection guide
  • RNA purification kit finder
  • PCR
  • Citations
  • Selection guides
  • Technical notes
  • FAQ
  • Cloning
  • In-Fusion Cloning general information
  • Primer design and other tools
  • In‑Fusion Cloning tips and FAQs
  • Applications and technical notes
  • Stem cell research
  • Overview
  • Protocols
  • Technical notes
  • Gene function
  • Gene editing
  • Viral transduction
  • T-cell transduction and culture
  • Inducible systems
  • Cell biology assays
  • Protein research
  • Capturem technology
  • Antibody immunoprecipitation
  • His-tag purification
  • Other tag purification
  • Expression systems
  • Antibodies and ELISA
  • Molecular diagnostics
  • Interview: adapting to change with Takara Bio
  • Applications
  • Solutions
  • Partnering
  • Webinar: Speeding up diagnostic development
  • Contact us
  • Vaccine development
  • Characterizing the viral genome and host response
  • Identifying and cloning vaccine targets
  • Expressing and purifying vaccine targets
  • Immunizing mice and optimizing vaccine targets
  • Pathogen detection
  • Sample prep
  • Detection methods
  • Identification and characterization
  • SARS-CoV-2
  • Antibiotic-resistant bacteria
  • Food crop pathogens
  • Waterborne disease outbreaks
  • Viral-induced cancer
  • Immunotherapy research
  • T-cell therapy
  • Antibody therapeutics
  • T-cell receptor profiling
  • TBI initiatives in cancer therapy
  • Cancer research
  • Sample prep from FFPE tissue
  • Sample prep from plasma
  • Cancer biomarker discovery
  • Cancer biomarker quantification
  • Single cancer cell analysis
  • Cancer genomics and epigenomics
  • HLA typing in cancer
  • Gene editing for cancer therapy/drug discovery
  • Alzheimer's disease research
  • Antibody engineering
  • Sample prep from FFPE tissue
  • Single-cell sequencing
  • Reproductive health technologies
  • Preimplantation genetic testing
  • ESM Collection Kit forms
Create a web account with us

Log in to enjoy additional benefits

Want to save this information?

An account with takarabio.com entitles you to extra features such as:

•  Creating and saving shopping carts
•  Keeping a list of your products of interest
•  Saving all of your favorite pages on the site*
•  Accessing restricted content

*Save favorites by clicking the star () in the top right corner of each page while you're logged in.

Create an account to get started

  • BioView blog
  • Automation
  • Cancer research
  • Career spotlights
  • Current events
  • Customer stories
  • Gene editing
  • Research news
  • Single-cell analysis
  • Stem cell research
  • Tips and troubleshooting
  • Women in STEM
  • That's Good Support!
  • About our blog
  • That's Good Science!
  • SMART-Seq Pro Biomarker Discovery Contest
  • DNA Day 2022
  • That's Good Science Podcast
  • Season one
  • Season two
  • Season three
  • Our brands
  • Takara
  • Clontech
  • Cellartis
  • Our history
  • Announcements
  • Events
  • Biomarker discovery events
  • Calendar
  • Conferences
  • Speak with us
  • Careers
  • Company benefits
  • Trademarks
  • License statements
  • Quality statement
  • Takara Bio affiliates & distributors
  • United States and Canada
  • China
  • Japan
  • Korea
  • Europe
  • India
  • Affiliates & distributors, by country
  • Need help?
  • Privacy request
  • Website FAQs

That's GOOD Science!

What does it take to generate good science? Careful planning, dedicated researchers, and the right tools. At Takara Bio, we thoughtfully develop best-in-class products to tackle your most challenging research problems, and have an expert team of technical support professionals to help you along the way, all at superior value.

Explore what makes good science possible

 Customer Login
 View Cart (0)
  • Home
  • Products
  • Services & Support
  • Learning centers
  • Applications
  • About
  • Contact us
  •  Customer Login
  • Register
  •  View Cart (0)

Takara Bio USA, Inc. provides kits, reagents, instruments, and services that help researchers explore questions about gene discovery, regulation, and function. As a member of the Takara Bio Group, TBUSA is part of a company that holds a leadership position in the global market and is committed to improving the human condition through biotechnology. Our mission is to develop high-quality innovative tools and services to accelerate discovery.

FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES (EXCEPT AS SPECIFICALLY NOTED).

Clontech, TaKaRa, cellartis

  • Products
  • Next-generation sequencing
  • Gene function
  • Stem cell research
  • Protein research
  • Diagnostic solutions
  • PCR
  • Cloning
  • Nucleic acid purification
  • Antibodies and ELISA
  • Real-time PCR
  • mRNA and cDNA synthesis
  • COVID-19 research
  • Next-generation sequencing
  • RNA-seq
  • DNA-seq
  • Single-cell NGS automation
  • Reproductive health
  • Bioinformatics tools
  • Whole genome amplification
  • Immune profiling
  • Epigenetics and small RNA sequencing
  • NGS accessories
  • Gene function
  • Gene editing
  • Viral transduction
  • Fluorescent proteins
  • T-cell transduction and culture
  • Tet-inducible expression systems
  • ProteoTuner protein control systems
  • iDimerize inducible protein interaction systems
  • Transfection reagents
  • Mammalian expression plasmids
  • Cell biology assays
  • Stem cell research
  • Media and supplements
  • Stem cells and stem cell-derived cells
  • Single-cell cloning of edited hiPS cells
  • Accessories
  • Protein research
  • Purification products
  • Two-hybrid and one-hybrid systems
  • Mass spectrometry reagents
  • Expression vectors & systems
  • Glycobiology
  • Antibodies and immunoprecipitation
  • SDS-PAGE & western blotting
  • Protein sequencing
  • Accessory enzymes
  • Diagnostic solutions
  • Infectious diseases
  • Reproductive health
  • PCR
  • Most popular polymerases
  • Standard PCR
  • High-yield PCR
  • High-fidelity PCR
  • Fast PCR
  • Long-range PCR
  • GC rich PCR
  • Direct PCR
  • PCR master mixes
  • Custom business friendly and automation-ready solutions
  • Molecular diagnostic products
  • GMP-grade products
  • Application-specific PCR
  • Other PCR-related products
  • PCR thermal cyclers
  • Cloning
  • In-Fusion seamless cloning
  • Competent cells
  • Ligation kits
  • Mutagenesis kits
  • Ligation enzymes
  • Restriction enzymes
  • Modifying enzymes
  • X-Gal and IPTG
  • Linkers, primers, and cloning vectors
  • Agarose gel electrophoresis
  • Nucleic acid extraction
  • Nucleic acid purification
  • Plasmid purification kits
  • Genomic DNA purification kits
  • DNA cleanup kits
  • RNA purification kits
  • RNA cleanup kits
  • Cell-free DNA purification kits
  • Viral DNA and RNA purification kits
  • Microbiome
  • Accessories and components
  • Antibodies and ELISA
  • Primary antibodies and ELISAs by research area
  • Secondary antibodies
  • Antibody and ELISA accessories
  • Fluorescent protein antibodies
  • Real-time PCR
  • Real-time PCR kits
  • Reverse transcription prior to qPCR
  • High-throughput qPCR solutions
  • Real-time PCR primer sets
  • References and standards for qPCR
  • RNA extraction and analysis for real-time qPCR
  • mRNA and cDNA synthesis
  • In vitro transcription
  • cDNA synthesis kits
  • Reverse transcriptases
  • RACE kits
  • Purified cDNA & genomic DNA
  • Purified total RNA and mRNA
  • mRNA and cDNA synthesis accessories
  • COVID-19 research
  • Viral detection with qPCR
  • SARS-CoV-2 pseudovirus
  • Human ACE2 stable cell line
  • Viral RNA isolation
  • Viral and host sequencing
  • Vaccine development
  • CRISPR screening
  • Drug discovery
  • Immune profiling
  • Publications
  • Services & Support
  • Instrument services
  • OEM & custom enzyme manufacturing
  • Stem cell services
  • Gene and cell therapy manufacturing
  • Customer service
  • Technical support
  • Sales
  • Shipping & delivery
  • Partnering & Licensing
  • Feedback
  • Webinars from Takara Bio
  • Vector information
  • Online tools
  • Instrument services
  • Apollo services
  • ICELL8 services
  • SmartChip services
  • OEM & custom enzyme manufacturing
  • Services
  • Quality
  • Expertise
  • OEM enzyme FAQs
  • Custom enzyme samples
  • Exploring OEM and custom enzyme partnerships
  • Stem cell services
  • Clinical-grade stem cell services
  • Research-grade stem cell services
  • Outsourcing stem cell-based disease model development
  • Gene and cell therapy manufacturing
  • Services
  • Facilities
  • Our process
  • Resources
  • Sales
  • Make an appointment with your sales rep
  • Webinars from Takara Bio
  • NGS: biomarkers and oncology
  • NGS: immunology
  • Stem cells
  • Real-time PCR
  • Gene function
  • Protein science
  • Vector information
  • Vector document overview
  • Vector document finder
  • Online tools
  • GoStix Plus FAQs
  • Learning centers
  • Automation systems
  • Next-generation sequencing
  • Gene function
  • Stem cell research
  • Protein research
  • PCR
  • Cloning
  • Nucleic acid purification
  • Antibodies and ELISA
  • Real-time PCR
  • cDNA synthesis
  • Automation systems
  • SmartChip Real-Time PCR System introduction
  • ICELL8 introduction
  • Apollo library prep system introduction
  • Next-generation sequencing
  • Product line overview
  • Technical notes
  • Featured kits
  • Technology and application overviews
  • FAQs and tips
  • DNA-seq protocols
  • Bioinformatics resources
  • Newsletters
  • Webinars
  • Citations
  • Posters
  • Gene function
  • Gene editing
  • Viral transduction
  • T-cell transduction and culture
  • Inducible systems
  • Transfection reagents
  • Fluorescent proteins
  • Cell biology assays
  • Stem cell research
  • Overview
  • Protocols
  • Applications
  • Technical notes
  • Posters
  • Webinars
  • Videos
  • FAQs
  • Citations
  • Selection guides
  • Protein research
  • Capturem technology
  • Antibody immunoprecipitation
  • His-tag purification
  • Other tag purification
  • Phosphoprotein and glycoprotein purification
  • Matchmaker Gold yeast two-hybrid systems
  • Expression systems
  • PCR
  • Citations
  • Selection guides
  • PCR enzyme brochure
  • Technical notes
  • FAQ
  • Go green with lyophilized enzymes
  • LA PCR technology
  • Cloning
  • In-Fusion Cloning general information
  • Primer design and other tools
  • In‑Fusion Cloning tips and FAQs
  • Applications and technical notes
  • Sign up to stay updated
  • Traditional molecular cloning
  • Nucleic acid purification
  • Nucleic acid extraction webinars
  • Product demonstration videos
  • Product finder
  • Plasmid kit selection guide
  • Plasmid purification
  • Genomic DNA purification
  • DNA/RNA cleanup and extraction
  • RNA purification
  • RNA purification kit finder
  • Viral DNA and RNA purification
  • Parallel DNA, RNA & protein
  • Automated DNA and RNA purification
  • Accessory selection guides
  • Microbiome
  • Antibodies and ELISA
  • Osteocalcin focus
  • Real-time PCR
  • Overview
  • Product finder
  • Reaction size guidelines
  • Real-time PCR products brochure
  • Real-time PCR tutorial videos
  • Guest webinar: extraction-free SARS-CoV-2 detection
  • Guest webinar: developing and validating molecular diagnostic tests
  • Technical notes
  • FAQs
  • cDNA synthesis
  • Premium total and poly A+ RNA
  • SMARTer RACE 5'/3' Kit
  • Cloning antibody variable regions
  • Applications
  • Molecular diagnostics
  • Pathogen detection
  • Vaccine development
  • Cancer research
  • Immunotherapy research
  • Alzheimer's disease research
  • Reproductive health technologies
  • Molecular diagnostics
  • Interview: adapting to change with Takara Bio
  • Applications
  • Solutions
  • Partnering
  • Webinar: Speeding up diagnostic development
  • Contact us
  • Pathogen detection
  • Sample prep
  • Detection methods
  • Identification and characterization
  • SARS-CoV-2
  • Antibiotic-resistant bacteria
  • Food crop pathogens
  • Waterborne disease outbreaks
  • Viral-induced cancer
  • Vaccine development
  • Characterizing the viral genome and host response
  • Identifying and cloning vaccine targets
  • Expressing and purifying vaccine targets
  • Immunizing mice and optimizing vaccine targets
  • Cancer research
  • Sample prep from FFPE tissue
  • Sample prep from plasma
  • Cancer biomarker discovery
  • Cancer biomarker quantification
  • Single cancer cell analysis
  • Cancer genomics and epigenomics
  • HLA typing in cancer
  • Gene editing for cancer therapy/drug discovery
  • Immunotherapy research
  • T-cell therapy
  • Antibody therapeutics
  • T-cell receptor profiling
  • TBI initiatives in cancer therapy
  • Alzheimer's disease research
  • Antibody engineering
  • Sample prep from FFPE tissue
  • Single-cell sequencing
  • Reproductive health technologies
  • Preimplantation genetic testing
  • ESM Collection Kit forms
  • About
  • BioView blog
  • That's Good Science!
  • Our brands
  • Our history
  • Announcements
  • Events
  • Careers
  • Trademarks
  • License statements
  • Quality and compliance
  • Takara Bio affiliates & distributors
  • Need help?
  • Website FAQs
  • DSS Takara Bio India Pvt. Ltd : Manufacturing
  • Our partners
  • Special offers
  • New products
  • BioView blog
  • Automation
  • Cancer research
  • Career spotlights
  • Current events
  • Customer stories
  • Gene editing
  • Research news
  • Single-cell analysis
  • Stem cell research
  • Tips and troubleshooting
  • Women in STEM
  • That's Good Support!
  • About our blog
  • That's Good Science!
  • SMART-Seq Pro Biomarker Discovery Contest
  • DNA Day 2022
  • That's Good Science Podcast
  • Season one
  • Season two
  • Season three
  • Our brands
  • Takara
  • Clontech
  • Cellartis
  • Events
  • Biomarker discovery events
  • Calendar
  • Conferences
  • Speak with us
  • Careers
  • Company benefits
  • Takara Bio affiliates & distributors
  • United States and Canada
  • China
  • Japan
  • Korea
  • Europe
  • India
  • Affiliates & distributors, by country
  • Need help?
  • Privacy request
  • Special offers
  • Baculovirus titration kits early access program
  • NGS bundle and save
  • TALON his-tag purification resin special offer
  • GoStix Plus special offers
  • PCR samples
  • Lab Essentials
  • Products
  • Services & Support
  • Learning centers
  • APPLICATIONS
  • About
  • Contact Us