PacBio生物資訊 教育訓練系列課程
PacBio生物資訊教育訓練系列課程
基礎課: A班6/27(二) ˙ B班6/28(三)
進階課: A班7/4 (二) ˙ B班7/11(二)
上課地點: 國家生技研究園區D 棟2 樓電腦教室
Technology seminar for 3D-Genomes
Exploring the Complexity of the Human Genome: Unveiling 3D Genome Structure and Structural Variants through Hi-C Technology
Thursday, 27th June 2023
2:00 PM – 3:00 PM
Venue: Room 208, Interdisciplinary Building
Speaker: Chui Li Leaw
CantataBio, LLC
Adaptor trimming for TruSeq DNA Methylation
1.
TruSeq DNA Methylation所使用的adapter序列與 TruSeq Single Index系統相同， bcl2fastq v2.2 guide在拆分過程中該軟體判斷adapter序列的嚴謹度(adapter stringency)定義如下：
The minimum match rate that triggers masking or trimming. This value is calculated as MatchCount / (MatchCount + MismatchCount). … The default value of 0.9 indicates that only reads with > 90% sequence identity with the adapter are trimmed.
(page. 14, bcl2fastq2-v2-20-software-guide)
由此研判，
25 mer 需有 23 mer 符合分析者給予的序列 (92%)
33 mer 需有 30 mer 符合分析者給予的序列 (90.9%)
才會被trim，兩者比例僅些微差異。
2.
起初由於TruSeq DNA Methylation的建議讀長較短( 2×75 or 2×100bp)，作為因應，提供的trimming序列亦較短；若使用較長的讀長如2×150或以上，亦可以使用33 mer；但整體而言，25 mer就可以達到trim adapter的效果。
Recommended read length: TruSeq DNA Methylation (illumina.com)
Special Discount For Users Paying by AS Intramural Funding
Dear Professors,
為響應中研院鼓勵老師使用院內經費申請核心設施的政策，本實驗室配合推出折扣方案：凡以院內轉帳付款的使用者，只要院內金額佔原總金額達 50% 以上，即可享有超值的優惠價格
第一期折扣方案：
於今年 (2020) 三月開始至五月底期間所申請的案件，若符合優惠條件，該案件的樣品製備及上機定序的費用可給予 2% off 折扣 (樣品 QC 不予折扣)
第二期折扣方案：
於今年 (2020) 六月開始之後所申請的案件，若符合優惠條件，該案件的樣品製備及上機定序的費用可給予 10% off 折扣 (樣品 QC 不予折扣)
以第二期折扣方案為例 (詳見範例如下)：
若某案件的費用總金額為 123.45 萬，只要其中 61.725 萬 (50%) 能夠以院內轉帳付款的話，即可達優惠條件，折扣後總金額降為 111.252 萬。因此，該筆款項便可以院內經費支付 61.725 萬，以院外經費支付 49.527 萬；或全額以院內經費支付尤佳
| Item ID | Item Description | Unit Price | Qty | Total | Total (in AS rate) |
|---|---|---|---|---|---|
| (S-Tb) | Low-input Stranded RNA Lib Prep, Ribo-zero | 7,800 | 66 | 514,800 | 463,320 (10% off) |
| (QC-QBR) | Qubit RNA | 80 | 66 | 5,280 | 5,280 |
| (QC-FAR) | Fragment Analyzer RNA | 1,570 | 6 | 9,420 | 9,420 |
| (HTPE125) | HiSeq HT v4, Paired End 2*125 | 117,500 | 6 | 705,000 | 634,500 (10% off) |
| 1,234,500 | 1,112,520 |
Sincerely,
NGS High Throughput Genomics Core
Biodiversity Research Center, Academia Sinica
Our New GridION Is Up And Running
Dear Professors,
We now offer Nanopore sequencing as a service with GridION Mk1, which allows a flexible seq run and analysis up to five individual flow cells. The average sequence data yields can vary widely and will mostly depend on the sample properties, while the current chemistry and software release enables to generate as much as 150 Gb of data output during a single GridION Mk1 run (30 Gb per cell).
The nanopore sequencing offers high-throughput long-read sequencing of both DNA and RNA samples, and also provides real-time data analysis. To learn more about the technology, please visit https://nanoporetech.com/how-it-works
Please kindly contact us if you are interested, and welcome to help spread the news!
Sincerely,
NGS High Throughput Genomics Core
Biodiversity Research Center, Academia Sinica
