.@nelsondl Didn't realize this - thanks for the correction!
9:21pm February 27th 2015 via Hootsuite in reply to
.@AndyLarrea Yes I did enjoy meeting you too Andy! I see there are no less than 7 events going on now!
VM: Tried via @nanopore as well - only alignments across, also amplification bias for larger 3 segments still remain #AGBT15
9:19pm February 27th 2015 via Hootsuite
VM: Able to get large amounts of avian virus to develop better methods of representation; template switch, 8 segments as multiplex #AGBT15
9:18pm February 27th 2015 via Hootsuite
VM:Now: used @Pacbio to CCS to close gaps from short-read assembly. Found uneven coverage in regions. #AGBT15
9:17pm February 27th 2015 via Hootsuite
VM:Used multiplex, degenerate and polyA primers; clinical monitoring over the years matched the seq data #AGBT15
9:14pm February 27th 2015 via Hootsuite
VM:Describes biology of influenza recombination of H and N subtypes and worldwide outbreaks. Samples collected 09 and 13-14 #AGBT15
9:13pm February 27th 2015 via Hootsuite
RT @KMS_Meltzy: Vince Magrini: a lifelong clever undergraduate #AGBT15
9:12pm February 27th 2015 via Twitter Web Client
Vince Magrini WashU (Introduced by K Dewar as a 'clever undergraduate') Influenza viral RNA-Seq by PacBio #AGBT15
9:09pm February 27th 2015 via Hootsuite
TS: Now want to improve pig genome as existing reference based on Sanger is 'a mess'. Today - N50 3MB #AGBT15
9:04pm February 27th 2015 via Hootsuite
TS: N50 is now 4.4MB w/add'l scaffolding. First assembly to go the highest quality you can. Want to do RNA-Seq and Iso-Seq #AGBT15
TS: Polished w/Quiver tool. Cp assemblies it's clear there are inversions / deletions missing from original assembly #AGBT15
9:01pm February 27th 2015 via Hootsuite
TS: Assembly: 194GB sequence, 38M reads; 5.1kb mean; max 40.3kb. 20x coverage of high-quality read went into Celera Assembler #AGBT15
8:59pm February 27th 2015 via Hootsuite
TS: Generated 57x coverage, P5/C3 w/309 cells, 11 libraries; about $120K cost in 78 machine-days. Collab w/S Koren at NBACC #AGBT15
8:58pm February 27th 2015 via Hootsuite
TS: 15K feral goats in only 57 sq miles; reduced to 250, Papadum goat in MD died unfortunately due to East Coast weather. #AGBT15
8:57pm February 27th 2015 via Hootsuite
TS: Tested for high homozygosity breed - chose San Clemente Island goat - 1875 brought to Calif island #AGBT15
8:56pm February 27th 2015 via Hootsuite
TS: Not bad for short-read; but GWAS evidenced problems - Tad Sonstegard & Curt Van Tassel (ARS in MD) - used 454 + ILMN mate-pair #AGBT
8:55pm February 27th 2015 via Hootsuite
TS:Goats had a single domestication event; 604 documented breeds worldwide. 2.9GB 2013 Nature Biotech http://t.co/lFDPKm4Oy1 #AGBT15
8:54pm February 27th 2015 via Hootsuite
TS:90% of goats are unimproved varieties. Introd genetically-selected goats into Africa have failed. Improve native goat populat'n #AGBT15
8:52pm February 27th 2015 via Hootsuite
TS: Funded by 'feed the future', USDA/USAID. Why goat? Leading source of income & protein 830M worldwide #AGBT15
Tim Smith, U.S. Meat Animal Research Center: A Genome Assembly of the Domestic Goat from 70x Coverage of SMRT Sequence #AGBT15
8:51pm February 27th 2015 via Hootsuite
SG:Q:How to correct a 2D read? A:Sorry - proprietary to @nanopore #AGBT15
8:50pm February 27th 2015 via Hootsuite
SG:Q:Cost of generating data? A:Can't talk about how much they pay; ~500MB at 90x coverage, 4 flowcells #AGBT15
8:47pm February 27th 2015 via Hootsuite
SG: Found 10K annotated transcripts; 5' TSS accuracy good #AGBT15
8:45pm February 27th 2015 via Hootsuite
SG: De novo assembly of ONT reads as a hybrid assembly; genomic elements >1300bp. Full-length isoforms: human cDNA 80K reads. #AGBT15
8:44pm February 27th 2015 via Hootsuite
SG: % of aligned reads - from 8% to 21% to top at 61%. #AGBT15
8:43pm February 27th 2015 via Hootsuite
SG:Analysis of 1024 types of 5-mers - GC% x fold difference graph some slope #AGBT15
8:40pm February 27th 2015 via Hootsuite
SG: The right aligner isn't a solved issue - lots of active research. She uses Blast for now. Reports some bias via G-C #AGBT15
8:39pm February 27th 2015 via Hootsuite
SG: Longest 2D read was 5.7kb. Shearing: unsheared DNA seems prone to breakage. 10Kb or 20Kb best sizes #AGBT15
8:37pm February 27th 2015 via Hootsuite
SG: Number of pores used directly impacts perf; 400 pores = >100MB data. Largest 191,145 bp long. "But not that useful' - no mapping #AGB
8:36pm February 27th 2015 via Hootsuite
SG:Yields range from 40MB, 200MB, 40MB, <<10MB (by library-prep type). Using his-tag protein for selection of hairpin adapters (!) #AG
8:34pm February 27th 2015 via Hootsuite
SG: 3 library formats - leader/leader adapter, hairpin/hairpin, leader + hairpin. "Flow cell yield has been highly variable" #AGBT15
8:32pm February 27th 2015 via Hootsuite
SG:Describes the MAP program for @nanopore and have had R6, R7 and R7.3 iterations to-date. Yeast W303 strain of S288C, some hum DNA #AGBT15
8:30pm February 27th 2015 via Hootsuite
Sara Goodwin Cold Spring Harbor: An in Depth Evaluation and Optimization of the Oxford MinION Device for de novo and cDNA Sequencing #AGBT15
8:29pm February 27th 2015 via Hootsuite
AK:Does RNA editing have a role in learning and memory? Hint at some evidence of cells in their circuits and behavior #AGBT15
8:24pm February 27th 2015 via Hootsuite
AK: 5HT induces synaptic genes in sensory neurons. Nascent RNAs are largely transcribed from demethylated genes #AGBT15
8:23pm February 27th 2015 via Hootsuite
AK: "Nothing in neuroscience makes sense except in the light of circuits" #AGBT15
8:20pm February 27th 2015 via Hootsuite
AK: Ratio of mC/C is similar across promoter elements; polyploid neruons are methylated the same way as diploid cells #AGBT15
8:19pm February 27th 2015 via Hootsuite
AK: ...have low gene-body and promoter methylation #AGBT15
8:18pm February 27th 2015 via Hootsuite
AK: Now looking at methylation (CG or CHG) across cell types. Saw mosaic pattern. But highly expressed neuron-spec genes... #AGBT15
AK: Three types of neurons examined: Glutamatergic sensory, serotonergic interneuron, cholinergic motor. Grow in Uracil-biotinylated #AGBT15
8:17pm February 27th 2015 via Hootsuite
AK: Following growth cones, look at up/down regulated genes. 5HT = serotonin, 'feel good' molecule; induces 5-mC down 5-hmC up #AGBT15
8:14pm February 27th 2015 via Hootsuite
AK: Long-term depression w/ FMRF. Further simplified - single sensory neuron, then motorneuron, look at behavior #AGBT15
8:13pm February 27th 2015 via Hootsuite
AK: Tail, gill still attached, can follow nerve, can condense from sensory neuron to motoneuron. Interneron 5-HT/NO (long-term sens) #AGBT15
8:12pm February 27th 2015 via Hootsuite
AK: Aplysia neurons as large as 1.1mm; like a bouquet of flowers, 10K neurons in brain, accessible, identifiable, same location #AGBT15
8:11pm February 27th 2015 via Hootsuite
AK: Roadmap Epigenomics Consortium: 'we still lack a systematic understanding' about cellular circuitry & differentiation #AGBT15
8:10pm February 27th 2015 via Hootsuite
AK: (Collaborator w/Leonid Moroz, highlighted here: http://t.co/oIzIo3yVuQ @iontorrent ) #AGBT15
8:09pm February 27th 2015 via Hootsuite
Andrea Kohn Univ FL Single-Cell Methylome Profiling: Integration of a Transcriptome and Methylome From Individual Identified Neurons #AGBT15
8:08pm February 27th 2015 via Hootsuite
AM: Now sequence activity map: fn of CD36 by aa position. Collapse to 3D structure from '08 Nature ref http://t.co/hqoXhLmL8N #AGBT15
8:06pm February 27th 2015 via Hootsuite
AM: Now: test in advance every mutation of PPAR-gamma. 9,576 var's, one var/pre-adipocyte cell. CD36 cell surface marker for assay #AGBT15
8:04pm February 27th 2015 via Hootsuite
