Li: DESeq dispersion looked poor; switched to Partek's tool, a mIR212/132 modulation of xcr demonstrated #RNASeq2014
9:21am June 19th 2014 via Hootsuite
Li: Analysis parameters do matter. 2nd case: map reads ~40%; using RPKM # detected genes differ substantially (3K vs 12K) #RNASeq2014
9:19am June 19th 2014 via Hootsuite
Li: Their discrepant DE results: dispersion est. driven by 1 out of 3 repl. samples; rec'd move to pooled estimate on DESeq #RNASeq2014
9:16am June 19th 2014 via Hootsuite
Li: Calc DESeq and EdgeR params for dispersion and quantile normalization: p<0.05, v. different numbers of genes #RNASeq2014
9:13am June 19th 2014 via Hootsuite
Li: Using ERCC, saw more scatter at lower conc; amplified material looked poor #RNASeq2014
9:11am June 19th 2014 via Hootsuite
Li: Used RiboMinus for rRNA removal (40% contam); 2nd round didn't help much. 100M-700M reads/sample. 10-30% map to exons #RNASeq2014
9:08am June 19th 2014 via Hootsuite
Li: Used SOLiD / 5500xl 50x35PE reads; after alignment they used Partek for gene- and isoform-level analysis #RNASeq2014
9:06am June 19th 2014 via Hootsuite
Li: Looking at WT / KO mice and diff exp genes; 5 total neural tissues along with microglial samples (need to amplify RNA) #RNASeq2014
9:04am June 19th 2014 via Hootsuite
Qingqin Li (J & J Biomarkers): "Comparison of RNA-Seq data analysis parameters using multiple datasets" #RNASeq2014
9:02am June 19th 2014 via Hootsuite
RT @kbradnam: My latest '101 questions with a bioinformatician' interview is Mr. Bioinformatics himself: @ewanbirney http://t.co/jGzuuBj1OL
8:20am June 19th 2014 via Hootsuite
RT @scicurious: Today at Eureka! Lab, I'm reviewing a science site for students, written by students themselves. http://t.co/Gz4h2dgtxU…
8:05am June 19th 2014 via Hootsuite
RT @engadget: 4SRS: the FBI built a list of Twitter slang to keep up with the kids http://t.co/GbjmysUyzB
7:10am June 19th 2014 via Hootsuite
NEJM reference RT @DrDanielSwan: Paper: Screening an Asymptomatic Person for Genetic Risk http://t.co/ht6zJV62au
6:10am June 19th 2014 via Hootsuite
RT @BioMickWatson: Gundlach nanopore technology, which @illumina licensed, sequences phi X http://t.co/rBqpgD7gtm
5:20am June 19th 2014 via Hootsuite
RT @TEDTalks: How great teachers create magic and inspire you to learn: http://t.co/qX83BfIJIH
4:20am June 19th 2014 via Hootsuite
MT @KevinADavies: First healthy baby (@razibkhan's son) born with entire genome decoded in advance | Tech Review http://t.co/RSgn7CdnXG
3:05am June 19th 2014 via Hootsuite
RT @GENbio: Clinically Actionable Genomics: From Sequencing to Personalized Medicine. View free webcast http://t.co/awyQJsNm0p
2:50am June 19th 2014 via Hootsuite
RT @DailyNewsGW: NIH, NSF Team to Help Biomedical Startups Translate Technologies to Market http://t.co/Lr22pc20DP
1:35am June 19th 2014 via Hootsuite
RT @ScienceNewsOrg: If the world is a computer, life is an algorithm http://t.co/vLPtdPLauR
12:25am June 19th 2014 via Hootsuite
RT @theNCI: The strongest risk factor for breast cancer is age. What are some other risk factors? http://t.co/dDAYTVOme0
11:25pm June 18th 2014 via Hootsuite
RT @TheAtlantic: How millennials are changing international travel http://t.co/EI94mDEath
10:50pm June 18th 2014 via Hootsuite
RT @Rndubois: Most states are cutting support for higher education pretty significantly: http://t.co/tlwwNfQbfv
10:20pm June 18th 2014 via Hootsuite
How to Anonymize Everything You Do Online | WIRED http://t.co/yf3zcCyXv4
9:10pm June 18th 2014 via Hootsuite
RT @findlungcancer: FDA Finally Proposes Social Media Guidelines http://t.co/F0voh5K1Wu via @WSJ #doctors20 #hcldr #hcsm #lcsm
8:25pm June 18th 2014 via Hootsuite
RT @mims: So here's what I consider the definitive take on disruption, by @monkbent http://t.co/RWhz1O7QPE
7:25pm June 18th 2014 via Hootsuite
RT @washingtonpost: Someone built a 114-foot tower entirely out of Legos http://t.co/uW06NkaWI7 http://t.co/H0Kja1Vpok
6:40pm June 18th 2014 via Hootsuite
RT @AMAnet: The slow demise of the frequent-flier program. (via @washingtonpost) #Biz #Travel #Management | http://t.co/9xpJHfSl6E
6:35pm June 18th 2014 via Hootsuite
RT @THebertMcGill: Social media and its effects... even the big companies are listening. http://t.co/yFiBOuhTXD
5:15pm June 18th 2014 via Hootsuite
Jackson: Listed validated methods / demonstrated methods / illumina-qualified as a partnership with them / NEB list also #RNASeq2014
4:30pm June 18th 2014 via Hootsuite
Jackson: What do customers want? Library quality, implementation, higher throughput, minimal hands-on time, flexibility #RNASeq2014
4:22pm June 18th 2014 via Hootsuite
Alisa Jackson (Beckman): "Automated solutions for highly reproducible RNA-Seq libraries for improved transcriptome analysis" #RNASeq2014
4:20pm June 18th 2014 via Hootsuite
Crosby:Q&A: Could RiboZero be obtaining pre-mRNAs? Perhaps. #RNASeq2014
4:17pm June 18th 2014 via Hootsuite
Crosby: Conclude: Arrays may be more sensitive than RNA-Seq (surprising); NGS lib prep can impact ability to detect fold change. #RNASeq2014
4:13pm June 18th 2014 via Hootsuite
Crosby: Conclude: different microarrays, different transcripts "only 1/2 RefSeq genes shared xcr pattersn" #RNASeq2014
4:12pm June 18th 2014 via Hootsuite
Crosby: Showed good RNA-Seq performance to the '7034'; 2x NGS lib preps (SMARTer, Epicentre) very similar #RNASeq2014
4:06pm June 18th 2014 via Hootsuite
Crosby: Microarray p-values <0.05; used an in-house developed direct labeling for microarrays; 30M reads/sample for RNA-Seq. #RNASeq2014
4:04pm June 18th 2014 via Hootsuite
Crosby: Mapped probes of microarrays to transcript patterns (7034 w/shared probes). Unpub. data #RNASeq2014
4:02pm June 18th 2014 via Hootsuite
Crosby: Took Agilent UHR RNA, human bone marrow RNA at dilutions; 4 microarray and 2 RNA-Seq lib prep; 33 genes via TaqMan #RNASeq2014
3:59pm June 18th 2014 via Hootsuite
.@Becky_Kusko RNA/DNA Integrated Analysis for Somatic Mutation detection on GitHub http://t.co/OH0LUqaAd6 #RNASeq2014
3:58pm June 18th 2014 via Hootsuite in reply to
Crosby: RNA-Seq can be 'what reviewers are looking for'. #RNASeq2014
3:57pm June 18th 2014 via Hootsuite
Crosby: GATC is a CRO-type facility, also has clinically validated cytogenetics, microarrays on down #RNASeq2014
3:54pm June 18th 2014 via Hootsuite
Seth Crosby (WashU): "RNA-Seq vs. Microarrays: a comparison as to which approach is most cost-effective for which situation" #RNASeq2014
3:52pm June 18th 2014 via Hootsuite
Yao: Q: any evidence of RNA editing? A: Haven't looked at it yet. #RNASeq2014
3:50pm June 18th 2014 via Hootsuite
Yao: "HR told me to put this slide" of 9 bioinformatics positions open at Merck. (So there's that.) #RNASeq2014
3:49pm June 18th 2014 via Hootsuite
Yao: Concludes 'RNA-Seq can be used for var discovery but not equivalent to DNA-Seq'. Will try GSNAP for RNA mapping #RNASeq2014
3:46pm June 18th 2014 via Hootsuite
Yao: 2nd strategy showed 92-94% concordance with same datasets; if dupl. weren't marked, went from 92 to 93% #RNASeq2014
3:45pm June 18th 2014 via Hootsuite
Yao: He used >20x cutoff for calling; 2nd approach used STAR instead of TopHat + duplicate marking for 2nd strategy #RNASeq2014
3:40pm June 18th 2014 via Hootsuite
Yao: After BWA-mem and TopHat alignment; DNA was 4x the reads: 100M vs 25M. Variant concordance was 74-77% betw. RNA/DNA #RNASeq2014
3:39pm June 18th 2014 via Hootsuite
Yao: Unpublished results so not a lot of detail; 22 samples, RNA-Seq at PE90bp and WES using Agilent 50MB at PE90bp #RNASeq2014
3:31pm June 18th 2014 via Hootsuite
Jianchao Yao (Merck): "Compare variant detection power between RNA-Seq and DNA-Seq" #RNASeq2014
3:29pm June 18th 2014 via Hootsuite
