A customer working on single-cell RNA-seq analysis contacted us to ask about building an environment based on PC-11781.
We are currently considering introducing a workstation that can run Cell Ranger locally, and the analysis scale is expected to be 3 cells x 20 samples, processed simultaneously or sequentially.
The client is looking for a configuration that will allow downstream analysis such as R/RStudio and Seurat to run smoothly, with a budget of less than 200 million yen and plans to secure separate storage for the system, data, and backup.
| CPU | Intel Xeon Gold 6530 2.10GHz(TB 4.00GHz) 32C/64T x 2 configuration |
| memory | Total 256GB DDR5 5600 REG ECC 16GB x 16 |
| Storage 1 | 2TB SSD M.2 NVMe Gen4 |
| Storage 2 | 4TB SSD M.2 NVMe Gen4 |
| Video | NVIDIA RTX A400 4GB (MiniDisplayPort x4) |
| network | on board (10GBase-T x2) |
| Housing + power supply | Tower type enclosure + 1500W 80PLUS PLATINUM |
| OS | Microsoft Windows 11 Professional 64bit |
| Storage 3 | External HDD 1 drive model 12TB (no RAID) |
| Storage 4 | 10TB HDD S-ATA (Life Science Campaign) |
| Others | Life Science Campaign Storage Services |
About CPU
To maximize the parallel processing performance of Cell Ranger, we installed two 32-core Xeon Gold 6530 processors, creating a two-CPU machine with a total of 64 cores.
Memory configuration
This configuration is equipped with sixteen 16GB memory modules and is designed to utilize all memory channels of each CPU.
The total memory capacity is 256GB, which meets the Cell Ranger's recommended requirements.
In addition, you can comfortably use downstream analysis such as R and Seurat as requested.
However, depending on the scale and content of the analysis, a larger memory capacity may be recommended.
In this configuration, all slots are filled, so if you want to add more, you will need to replace them with modules of larger capacity.
Reference: System Requirements _ 10x Genomics Official Support
About storage
Data protection has been enhanced by adding a 2TB M.2 drive for the system, a 4TB M.2 drive for storing data used in analysis, and an external 12TB HDD for backup purposes.
We can also suggest NAS or additional storage in preparation for future data increases.
Furthermore, this timeLife Science Researcher Support CampaignIf you use this service, we will add one 10TB HDD free of charge.
In large-scale single-cell analysis, the number of samples and the amount of data increase rapidly.
This campaign is a great opportunity to secure storage at no additional cost.
For more details about the campaign, please see the link below:
About GPU
This time, we are not considering machine learning or GPU accelerators, so we adopted the entry-level RTX A400 for screen drawing.
For those who are active in these fields
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Tegara's custom-made PC production service not only caters to initial use, but also supports system expansion in anticipation of future expansion of research scale.
We not only propose configurations that meet various software requirements, but also accept consultations regarding the construction of an entire research environment.
Please feel free to contact us and we will provide the best solution to suit your needs.
KeywordWhat is Cell Ranger? Cell Ranger is software that can analyze single-cell RNA sequencing data obtained from 10x Genomics' Chromium platform in bulk.
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