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Sam White wrote a new post, DNA Methylation Analysis – Bismark Pipeline on All Olympia oyster BSseq Datasets, on the site Sam's Notebook 3 days, 2 hours ago
Bismark analysis of all of our current Olympia oyster (Ostrea lurida) DNA methylation high-throughput sequencing data.
Analysis was run on Emu (Ubuntu 16.04LTS, Apple Xserve). The primary analysis took ~14 days […]
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Sam White wrote a new post, Data Received – Geoduck Metagenome HiSeqX Data, on the site Sam's Notebook 1 week, 3 days ago
Received the data from the geoduck metagenome libraries that I prepared and were sequenced at the Northwest Genomics Center at UW on the HiSeqX (Illumina) – PE 151bp.
FastQ files are being transferred to <a […]
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Sam White wrote a new post, RNA Isolation & Quantificaiton – Tanner Crab Hemolymph, on the site Sam's Notebook 1 week, 3 days ago
Isolated RNA from 40 Tanner crab hemolymph samples selected by Grace with the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s protocol, with the following modifications:
- Added mercaptoethanol […]
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Sam White wrote a new post, Genome Annoation – Olympia oyster genome annotation results #02, on the site Sam's Notebook 1 week, 4 days ago
Yesterday, I annotated our Olympia oyster genome using WQ-MAKER in just 7hrs!.See that link for run setup and configuration. They are essentially the same, except for the change I’ll discuss below.
The results […]
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Sam White wrote a new post, Genome Annoation – Olympia oyster genome annotation results #01, on the site Sam's Notebook 1 week, 4 days ago
Yesterday, I annotated our Olympia oyster genome using WQ-MAKER in just 7hrs!.
See that link for run setup and configuration.
RESULTS
Before proceeding further, it should be noted that I neglected to provide […]
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Sam White wrote a new post, Genome Annotation – Olympia oyster genome complete – brief note, on the site Sam's Notebook 1 week, 5 days ago
Whoa! Genome annotation using Jetstream/WQ-MAKER that I started this morning is complete!! Only 7hrs!More detailed entry coming once I move files off of Jetstream and have a chance to look at things.
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Sam White wrote a new post, Genome Annotation – Olympia oyster genome using WQ-MAKER Instance on Jetstream, on the site Sam's Notebook 1 week, 5 days ago
Yesterday, our Xsede Startup Application (Google Doc) got approval for 100,000 Service Units (SUs) and 1TB of disk space on Xsede/Atmosphere/Jetstream (or, whatever it’s actually called!). The approval happened […] -
ADAMS changed their profile picture 2 weeks, 2 days ago
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ADAMS’s profile was updated 2 weeks, 2 days ago
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ADAMS posted an update 2 weeks, 2 days ago
[zymo gel extraction kit] I recently was having problems with this kit. The purified products always have high absorbance at 230nm or less. After contacting their technical support and practiced couple times, I finally figured out a way to avoid this. (1) do not use more than 400 mg of gel for each column. The columns seems to have a limited…[Read more]
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Sam White wrote a new post, Bioanalyzer – Tanner Crab RNA Isolated with RNeasy Plus Mini Kit, on the site Sam's Notebook 2 weeks, 4 days ago
Ran the four Tanner crab RNA samples that I isolated yesterday on the Seeb Lab Bioanalyzer 2100 (Agilent) using the RNA Pico 6000 Kit.Samples were run following kit protocol:
- Chip priming station in Position C […]
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ADAMS became a registered member 2 weeks, 4 days ago
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Sam White wrote a new post, RNA Cleanup – Tanner Crab RNA, on the site Sam's Notebook 2 weeks, 5 days ago
In a continued attempt to figure out what we can do about the tanner crab RNA, Steven tasked me with using an RNeasy Kit to cleanup some existing RNA.Here’re the samples grace provided:
All of the RNA had […]
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Sam White wrote a new post, RNA Isolation – Tanner Crab Hemolymph Using RNeasy Plus Mini Kit, on the site Sam's Notebook 2 weeks, 5 days ago
Tanner crab RNA has proved a bit troublesome. As such, Steven asked me to try isolating some RNA using the RNeasy Plus Mini Kit (Qiagen) to see how things would turn out.Grace provided me with the following […]
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Sam White wrote a new post, Mox – Over quota: Olympia oyster genome annotation progress (using Maker 2.31.10), on the site Sam's Notebook 2 weeks, 6 days ago
UPDATE 20180730Per this GitHub Issue, Steven has cleared out files.
Additionally, it appears that my job has just continued from where it was stuck. Very nice!
ORIGINAL POST IS BELOW
Well, this is an issue. […]
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Sam White wrote a new post, RNA Cleanup – Tanner Crab RNA Pools, on the site Sam's Notebook 1 month ago
Grace had previously pooled a set of crab RNA in preparation for RNAseq. Yesterday, we/she concentrated the samples and then quantified them. Unfortunately, Qubit results were not good (concentrations were far […] -
Danny Garside became a registered member 1 month ago
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Sam White wrote a new post, Mox – Olympia oyster genome annotation progress (using Maker 2.31.10), on the site Sam's Notebook 1 month, 1 week ago
TL;DR – It appears to be continuing where it left off!I decided to spend some time to figure out what was actually happening, as it’s clear that the annotation process is going to need some additional time to […]
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Sam White wrote a new post, Mox – Password-less SSH!, on the site Sam's Notebook 1 month, 1 week ago
The high performance computing (HPC) cluster (called Mox) at Univ. of Washington (UW) frustratingly requires a password when SSH-ing, even when SSH keys are in use. I have a lengthy, unintelligable password that […]
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Sam White wrote a new post, Ubuntu – Fix “No Video Signal” Issue on Emu/Roadrunner, on the site Sam's Notebook 1 month, 2 weeks ago
Both Apple Xserves (Emu/Roadrunner) running Ubuntu (16.04LTS) experienced the same issue – the monitor would indicate “No Video Signal”, would go dark, and wasn’t responsive to keyboard/mouse movements. However, […]
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