Tonge: No homopolymer errors affected their OTU assignments; reads are not proportional (due to copy var in underlying genomes) #IWT14
7:13am September 12th 2014 via Hootsuite
Tonge: Operational Taxonomic Units (OTU) sequence info shown - observed that ITS1 got 7/8. #IWT14
7:10am September 12th 2014 via Hootsuite
Tonge: (cont) then cluster. OTU formation: identity of 0.97. Test set not expected 8, it was 24-16 (based upon the IT1/2/LSU region) #IWT14
7:08am September 12th 2014 via Hootsuite
Tonge: Informatics workflow: trim, de-replicate identical sequences, 'denoise' data (if within 1% of each other consider same)... #IWT14
7:05am September 12th 2014 via Hootsuite
Tonge: Ave sequencing quality of Q30, on an early 400bp kit, with V1 314 chips. #IWT14
7:04am September 12th 2014 via Hootsuite
Tonge: 600K-800K reads on a 314 chip; trimmed products to result in 280K-630K final reads; quality graph shown; plans to use Hi-Q #IWT14
7:03am September 12th 2014 via Hootsuite
Tonge: Proof study: 8 pure fungal cultures, spores produced, DNA isolated, equimolar mix. Amplified one at a time, separate 314 chips #IWT14
6:59am September 12th 2014 via Hootsuite
Tonge: Lists bioinformatics tools he uses: FASTQC, CutAdapt, USEARCH, QIIME, Mothur, UPARSE #IWT14
6:58am September 12th 2014 via Hootsuite
Tonge: Compared classical cloning and Sanger sequencing approach "not appropriate"; same-day on PGM. Suitable for env samples #IWT14
6:56am September 12th 2014 via Hootsuite
Tonge: Developed Ion adapter-fusion primers, with P1 and A adapters. But the primers get large - 49 + 43-mers. Added barcodes too #IWT14
6:55am September 12th 2014 via Hootsuite
Tonge: Nuclear ribosomal repeat unit (ITS1/2 and LSU); LSU for distant fungi, ITS1/2 for genus/species level #IWT14
6:53am September 12th 2014 via Hootsuite
Tonge: Recent work published Apr 14 PLOS One http://t.co/w5mfdvrJpY Similar to 16S, amplified specific regions of fungal genome #IWT14
6:51am September 12th 2014 via Hootsuite
Tonge: Started work on SOLiD with personalized medicine and biomarkers; now fungi speciation in a public health context #IWT14
6:50am September 12th 2014 via Hootsuite
Last up: Dan Tonge (Univ Stafford): "Amplicon-driven fungal metagenomics" #IWT14
6:48am September 12th 2014 via Hootsuite
Carli: Discuva has a 1-day conference Sept 24 in Cambridge UK "One Bug One Drug" (PDF) http://t.co/KEr1EB0PJB #IWT14
6:46am September 12th 2014 via Hootsuite
Carli: ID of candidate target via Ion Proton sequencer, to determine mechanism of compound action. SETI method Tn knockouts #IWT14
6:28am September 12th 2014 via Hootsuite
Carli: Selective Antibiotic Target Identification; antibiotic resistance a major problem; focus on bact essential genes #IWT14
6:25am September 12th 2014 via Hootsuite
Natasha Carli, Joana Martins (Discuva Ltd Cambrdige) "Discovery of new antibiotics using transposon-insertion sequencing" #IWT14
6:19am September 12th 2014 via Hootsuite
Murphy: Alex Laird 2013 review "5-hydroxymethylcytosine profiling as an indicator of cellular state" PubMed http://t.co/1TlihucOw4
6:04am September 12th 2014 via Hootsuite
Murphy: #IWT14 Thomson 2013 NAR reference comparing 3 hydroxymethylC sequencing methods http://t.co/fQWYppPhii
5:14am September 12th 2014 via Hootsuite
Murphy: (Showed a troubleshooting exercise with inconsistent promoter CpG island signal) Believes there's bias in their WGA #IWT14
5:12am September 12th 2014 via Hootsuite
Murphy: Replicates have R about 0.6; showed cross-method comparison; compared to HiSeq platform (very similar) #IWT14
5:06am September 12th 2014 via Hootsuite
Murphy: Showed data, has done 24 samples across 24 PI chips; shows good vs poor read distribution (i.e. bimodal short ones) #IWT14
Murphy: Maps to mouse reference, filter reads <50bp, normalization, 200bp non-overlapping read counts across genome #IWT14
5:05am September 12th 2014 via Hootsuite
Murphy: His post-doc 'data within a week' 'he's thrilled with this' due to speed of Proton #IWT14
5:04am September 12th 2014 via Hootsuite
Murphy: Mouse DNA, uses a modified meDIP protocol; single strand to WGS after pull-down; modified library prep #IWT14
5:03am September 12th 2014 via Hootsuite
Murphy: Reduction of 5hmC importance in cancer; modification of protocol (Thomson 2013 NAR). 3 methods compared #IWT14
5:02am September 12th 2014 via Hootsuite
Murphy: Points out methylation in the gene body; Peter Laird's work (Epigenetics rev 2013) #IWT14 BtB Blog http://t.co/y42NVx8fGC
5:01am September 12th 2014 via Hootsuite
Murphy: #IWT14 Refers to the importance of 5hmC, an overlooked methylation mark http://t.co/nO07kQpuDz
5:00am September 12th 2014 via Hootsuite
Murphy: Methylation via sequencing can distinguish between 5mC and 5hmC; other adv in chart (comparing microarray to NGS) #IWT14
4:57am September 12th 2014 via Hootsuite
Murphy: Many 450K methylation arrays; recent work on Crohns (PubMed) http://t.co/5jTQiHE5xn #IWT14
4:56am September 12th 2014 via Hootsuite
Murphy: "I really like the flexibility" of the Ion Torrent platforms. Ion Chef "It's great" #IWT14
4:54am September 12th 2014 via Hootsuite
Murphy: They have biobanking, sample processing, and analysis (historically genotyping via qPCR, microarrays, more on PGM / Proton #IWT14
Lee Murphy (Wellcome Trust, Western Hosp. Edinburgh) "ChIP-Seq analysis on the Ion Proton System" #IWT14
4:52am September 12th 2014 via Hootsuite
Mangion:Q: Change in reference db's? A: You can upload references in TS; in Ion Reporter does take time, when it stabilizes #IWT14
4:48am September 12th 2014 via Hootsuite
Mangion: Has 'Training Beyond the Box' - Genomics in Medicine, Bioinf. for molecular biologiests #IWT14 http://t.co/NsxWiIB6R9
4:46am September 12th 2014 via Hootsuite
Mangion: Points out availability of IT Professional Services; obstacles to implementation disappear when they get involved #IWT14
4:43am September 12th 2014 via Hootsuite
Mangion: A balance of sensitivity (low stringency) and specificity (high stringency); one size does not fit all #IWT14
4:39am September 12th 2014 via Hootsuite
Mangion: ("dept" in prior post = "dependent") #IWT14
4:38am September 12th 2014 via Hootsuite
Mangion: Mentions NIST Genome in a Bottle; showed sens shooting up dept on var caller #IWT14 Blog post: http://t.co/jTjOTYbbCD
4:37am September 12th 2014 via Hootsuite
Mangion: Novel insertion - example filtered out due to insufficient coverage (11x instead of default param 15x) #IWT14
4:36am September 12th 2014 via Hootsuite
Mangion: Sometimes annotations in db's as 'hotspot'; a putative del in homopol on L end. Filtered out due to 'common signal shift' #IWT14
4:34am September 12th 2014 via Hootsuite
Mangion: Mentions HiQ: for smaller panels, software is already dealing with indels like these, so improvement on these panels limited #IWT14
4:32am September 12th 2014 via Hootsuite
Mangion: Strand bias (137 alt allele of 1200) + position of del in homopol = evaluated and rejected #IWT14
4:31am September 12th 2014 via Hootsuite
Mangion: "Source:novel" is a DEL, coverage ~1200, shows strand bias, more info in flow space for more detail. Del in homopol 5x "G" #IWT14
4:30am September 12th 2014 via Hootsuite
Mangion: Another "Source:Hotspot" forces a genotype call, but no data is there (homozygous to ref), 0% freq #IWT14
4:29am September 12th 2014 via Hootsuite
Mangion: "Source: Hotspot" goes straight to evaluation; example GG to TT at 2.3%, quality score is relatively low #IWT14
4:28am September 12th 2014 via Hootsuite
Mangion: 'Source: Novel' variant is a lablel when it lies outside a hotspot region #IWT14
4:27am September 12th 2014 via Hootsuite
Mangion: "What is the hypothesis to test?" is the consideration - what's involved with changing parameters in TVC #IWT14
4:24am September 12th 2014 via Hootsuite
Mangion: TVC (variant caller) Evaluation of candidate var's have many parameters; many caveats to change from defaults #IWT14
4:23am September 12th 2014 via Hootsuite
