Work Log 4/19

Transcript

1. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine Work Log 04/19 D u p l i c a t e d re a d s , R N A - S e q  N G S s e r v i c e @ Ta i w a n  pic from Maentis
2. Duplicated reads often viewed as artifacts •  It’s unlikely to get two identical sequences in a same run •  If that happens, most possibly it is caused by reading a same cDNA fragments twice •  If overall # of identical sequence >> 2, the sample is likely either •  contaminated (Ex PCR primer, …) •  running too many PCR cycles (over-amplification) •  having too less unique fragments (over-sequencing) •  If we back to our sequence data … •  use result by FastQC Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 2
3. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 3 •  Duplication level is slightly higher => reduce PCR cycle 
4. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine NGS Services @Taiwan Focused on Northern Taiwan pic from Maentis
5. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 5 data from http://omicsmaps.com/ Taiwan is one of top 20 countries having the most sequencers or sequence service providers
6. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 6 data from http://omicsmaps.com/ National Tsing Hua University 1 x GA2 Chang Gung University Genomics Core (長庚) 1 x SOLiD, 1 x Ion Torrent yourgene bioscience (有勁生技) 1 x GA2, 1 x HiSeq Integrated Core Facility for Functional Genomics 1 x SOLiD 3/4 (CGM) New information can self-upload to here Yang Ming U Genome Research Center 2 x 454, 1 x Illumina GA2, 1 x HiSeq, 1 x MiSeq NTOU (海洋) 1 x 454
7. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 7 NTU CGM 4 x SOLiD3/4 NTU-TechComm 1 x SOLiD, 1 x MiSeq Biodiversity Research Center, Academia Sinica 1 x 454, 2 x GA2,1 x SOLiD3/4 IBMS, Academia Sinica 1 x 454, 1 x HiSeq ( 幫他們更新了 xd） MissionBio (明欣生技) 2 x SOLiD3/4, 1 x 454, 1 x Ion Torrent Tri-ibiotech, inc. (源資生技) 1 x SOLiD, 1 x MiSeq Genomics BioSci&Tech 1 x SOLiD, 2 x Ion Torrent 1 x Roche/454
8. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 8 Organization NGS service HiSeq $ Others $ Note 清華大學 N - - 長庚基因體中心 N - - 有勁生技公司 Y ? ? 基因微陣列 @NTU CGM Y - GAII RNA 80K/lane 榮陽基因體中心 Y 50-150 bp 40-130K/lane 454 0.2-1M bp 80K-313K 生科院 TechComm Y - project based 我們 @NTU CGM Y ? ? 中研院基因體 N - - 國家基因體中心 Y 100-150 bp 93-10K/lane 454 (same) data analysis .5K-8K ?!  MissionBio  Y - project based Tri-ibiotech Y - project based Genomics  Y - project based
9. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 9 2012.12 from http://flxlexblog.wordpress.com/
10. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine pic by Shuttershock Appistry’s solution @AACR 2013 NGS Pipeline Setup
11. long chat 3 repeats @AACR •  It is a big old company •  for parallel computing infrastructure •  starting bio industry in these two years Their solution is compact and user-friendly, •  use Galaxy to combined all tools •  monitor and deploy computing resources by their own app Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 11
12. Their customers Brigham Young University, Brown University, Center for Rare Jewish Genetic Disorders, Clearent, CHOP – Children’s Hospital of Philadelphia, Emory Winship Cancer Institute, FedEx, The Jackson Laboratory, JP Morgan, Lombardi Comprehensive Cancer Center, National Information Solutions Cooperative (NISC), Next Century Corporation, Northrop Grumman, RaNA Therapeutics, SAIC, Stanford University School of Medicine, State Street Corporation, Tygart, USIC, U.L.B. Universite Libre de Burxelles, UC Davis Genome Center, The University of California- Davis, The University of Colorado-Boulder, University of Iowa, University of Iowa Children’s Hospital, The University of Missouri, University of Pennsylvania, Western Australian Institute for Medical Research, University of Wisconsin, Yale University Cancer Center Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 12
13. Galaxy workflow Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 13 from http://gmod.org/wiki/Galaxy_Tutorial_2010
14. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 14 What’s Next?! Future Work on RNA-Seq pipeline pic from Maentis
15. RNA-Seq workflow Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 15