Trapnell #AGBT19 Monocle 2 works with thousands of cells, not for millions. tSNE to umap coordinates, shows 2D to 3… https://t.co/xgveTA6TbL
1:42pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 61 embryos over 5d. Note even 1x cell coverage: from 2M cells: shows colors in 3D changing over ti… https://t.co/jaLqW8MU7k
1:40pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 (Split pooling idea described last night, similar). Can take all RNA-seq reads, and determine what… https://t.co/Uto0CitewX
1:38pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 And then learning the trajectory. Combinatorial indexing - take cells, solubilize, distribute, per… https://t.co/pqb6pLH1TW
1:36pm March 2nd 2019 via Twitter Web Client
Trapnell #AGBT19 Shows a video illustrating Waddington's landscape - illustrating developmental landscapes using sc… https://t.co/wpDOw3usbL
1:35pm March 2nd 2019 via Twitter Web Client
Cole Trapnell (Univ Washington) #AGBT19 Single-cell transcriptome analysis at whole-embryo scale
1:33pm March 2nd 2019 via Twitter Web Client
Levy #AGBT19 Rapid Run mode gap now closed with S-prime (SP) cell. Same readlengths, 150bp vs 250bp inserts hard to keep head-to-head.
12:41pm March 2nd 2019 via Twitter Web Client
Levy #AGBT19 Support of Orien - research network for data sharing. RNA-Seq now 50M-100M. Exomes now 100x-400x. WGS… https://t.co/5Rv9ysDtG9
12:38pm March 2nd 2019 via Twitter Web Client
Levy #AGBT19 Shows charts on pricing and outputs. https://t.co/FfHoJgva2n
12:37pm March 2nd 2019 via Twitter for iPhone
Levy #AGBT19 Plots out the growth of Illumina platforms. NovaSeq called 'the Keureg of sequencers'. Reagent managem… https://t.co/MistDkkTfs
12:35pm March 2nd 2019 via Twitter Web Client
Levy #AGBT19 Shows one of his boys on Microarray, then 454, SOLiD, PGM, HiSeq, then iSeq/NovaSeq.
12:33pm March 2nd 2019 via Twitter Web Client
Shawn Levy (Hudson Alpha) #AGBT19 Will be talking about transition to NovaSeq 6000; longer reads, 'holism of sequen… https://t.co/nerccmWYoC
12:31pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 the value of the NovaSeq 6000, 325-400GB, 38h, $13.75/Gb vs the HiSeq 2500 RR at $41.73.
12:29pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 Shows 2x251bp on the iSeq 100. NextSeq 550 update: the v2.5 kits ambient ship, new control SW to sc… https://t.co/WKqGoPVFP1
12:25pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 6.5h to pooled library; flexible to panel options and your own too. Points out Rady world record 19… https://t.co/9RBP86UCtU
12:20pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 Now no index repeated. Nextera Flex compared to XT in terms of GC coverage; compared to microbiome mock mixture.
12:15pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 Robust to DNA input - bead-based normalization. No need for library quant. Revamping indexing strat… https://t.co/RO7PYeyrSc
12:12pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 7y ago Epicentre purchased; Nextera XT best-selling; attached to beads gives control.
12:10pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 In Q3 of 2018 the amount of capacity shipped was the entire year's of 2016.
12:09pm March 2nd 2019 via Twitter Web Client
Schroth #AGBT19 Sequencing capacity shipped by Illumina https://t.co/1m2PIXNS9W
12:08pm March 2nd 2019 via Twitter for iPhone
Gary Schroth (Illumina) Transforming the future of genomics, together @Genomics_Guy #AGBT19
12:07pm March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 Targeted long-read for 1MB would be great... Openly released just now: https://t.co/pXVKpqdgII Com… https://t.co/yC5K9Jh7CK
11:46am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 Is it correct? Showed some validation data via BstEII southern blot and other data. T2T assembly o… https://t.co/mTx6qzXOg2
11:45am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 The last gap: chrX. Found unique structural vars from PacBio reads, then unique k-mers confirmed v… https://t.co/slbGVR7Lqh
11:43am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 55x copies (165kb array) DXZ4 gene family, quantified with ddPCR.
11:41am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 First complete chromosome - manual gap closure, correct repeat collapse. Bionano map showed missing repeat units.
Phillippy #AGB19 Shows bands of contigs, and then '19 the contrast. Contigs in '02 was 0.15MB (?) now 75MB. Chose chrX
11:39am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 Continual sampling to high coverage: enough sampling will cover the repeat in question. CHM13 from… https://t.co/cCPH37hi0g
11:38am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 Shows read-length distribution - 50% of bases for ONT and BioNano are >100Kb. Nanopore UL read length is long-tailed.
11:37am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 30x nanopore ultra-long, 60x Pacbio for polishing, 50x 10X Genomics polishing, BioNano structural var.
11:36am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 @pathogenomenick and @mattloose have a Long Read Club (shirts!). Karen and Adam have formed a T2T consortium.
Phillippy #AGB19 Read coverage and accuracy matter too. MinION device - now readlengths >1 Mbp possible. If 8cm fis… https://t.co/JSXW65Z
11:34am March 2nd 2019 via Twitter Web Client
RT @aphillippy: Presenting "Telomere-to-telomere assembly of a complete human X chromosome" today at 11:30am #AGBT19. Slides: https://t.co/…
11:33am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 AGBT 2012: closed bacterial genomes with the help of long reads. (7kb rDNA repeats in microbes). S… https://t.co/Zo2ohDUALO
Phillippy #AGB19 Collaboration with Karen Miga (UCSC); @khmiga @aphillippy Repeats are long, reads are short. Stade… https://t.co/fsmMVQFhX2
11:32am March 2nd 2019 via Twitter Web Client
Phillippy #AGB19 The human reference genome is incomplete. 368 unresolved issues, 102 gaps. Gaps have impt info; mi… https://t.co/Wczilgvwmd
11:30am March 2nd 2019 via Twitter Web Client
Adam Phillippy (NHGRI) #AGBT19 Telomere-to-telomere assembly of a complete human X chromosome
11:29am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 The preprint of this work presented this AM https://t.co/s0cXj4FaJ4
11:27am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 Transformed metric LOEUF decile - constraint merics for protein-protein interactions, gene expression, disease assoc
11:23am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 Testing the model for severe ID - obs vs expected freq, LoF are strongly depleted. Perhaps embryonic lethal gene.
11:20am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 Dev tool called LOFTEE - variant-effect predictor not using freq. https://t.co/SAoYf53TUm Varian… https://t.co/sJjND8RrMc
11:17am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 'Staggering amounts of variation' - 250M vars in 15.7 WGS; 15M vars in 125.7M WES. And predict some 513K LoF variants.
11:16am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 Sub-continental ancestry. https://t.co/n73T95B4U3
11:15am March 2nd 2019 via Twitter for iPhone
Karczewski #AGBT19 Novel QC pipeline https://t.co/d6Ubr2deHk Shows plot of representation
11:15am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 New framework called https://t.co/vZpDeV60VH scaling to 1000's of CPUs. gnomAD site: https://t.co/esVGgeGtCn
11:13am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 However ID true LoF is hard: rarity, and enriched for artifacts. Catalogues - gnomAD 125.7K WES… https://t.co/7PMtY84GY6
11:12am March 2nd 2019 via Twitter Web Client
Karczewski #AGBT19 Range of LoF impact - from embryonic lethal, haploinsuff, recessive, complex disease, nonessenti… https://t.co/7F10ecFoFq
11:11am March 2nd 2019 via Twitter Web Client
Konrad Karczewski (Broad Inst) #AGB19 Variation across 141,456 human exomes and genomes reveals the spectrum of los… https://t.co/YBngeigF59
11:10am March 2nd 2019 via Twitter Web Client
RT @TPU_ICR: AM. A higher proportion of HIV+ patients have higher tumour grade. Seq used - using WGS, WES, panel, mRNA seq, ChIP and Array…
11:01am March 2nd 2019 via Hootsuite Inc.
Hey #AGBT19 I just do what Eva tells me to - come down to @QIAGENscience to take the challenge in Seagrape1. https://t.co/h6NAkZ6JhG
10:46am March 2nd 2019 via Twitter for iPhone
