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Sam White wrote a new post, Genome Assembly – Olympia oyster Illumina & PacBio reads using MaSuRCA, on the site Sam's Notebook 1 hour, 59 minutes ago
Ran this on Mox (hyak) node.Create single PacBio FASTA file:
list of PacBio files:
m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq […]
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Sam White wrote a new post, Software Installation – MaSuRCA v3.2.3 Assembler on Mox (Hyak), on the site Sam's Notebook 5 hours, 16 minutes ago
Saw this tweet this morning and thought this would be good to try out for our Olympia oyster genome assemblies, as it will handle “hybrid” assemblies (i.e. short-reads and long reads):The latest verison of the […]
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Gabriela became a registered member 5 hours, 45 minutes ago
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Sam White wrote a new post, Fail – Directory Contents Deleted!, on the site Sam's Notebook 1 day, 1 hour ago
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Sam White wrote a new post, Samples Received – Green Abalone Slides from Fio Micheli, on the site Sam's Notebook 3 days, 4 hours ago
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Sam White wrote a new post, DNA Isolation – Ava Withering Syndrome Transmission Study Tissues, on the site Sam's Notebook 3 days, 5 hours ago
Isolated DNA from 17 red abalone digestive gland tissue samples.
Tissue was weighed, minced with a razor blade, and transferred to 2mL snap cap tube containing 1mL of InhibtEX Buffer.
DNA was extracted using the […]
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Sam White wrote a new post, DNA Isolation – Ava Withering Syndrome Transmission Study Tissues, on the site Sam's Notebook 1 week ago
Isolated DNA from 96 red abalone digestive gland tissue samples.
Tissue was weighed, minced with a razor blade, and transferred to 2mL snap cap tube containing 1mL of InhibtEX Buffer.
DNA was extracted using the […]
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Sam White wrote a new post, Data Management – Convert Oly PacBio H5 to FASTQ, on the site Sam's Notebook 1 week, 3 days ago
After working with all of this Olympia oyster genome sequencing data, I remembered that we had an old, singular PacBio SMRT cell file (from June 2013). This file didn’t seem to be included in any recent assemblies […]
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Pardon us, Sam,
This is our final test of new code which sends you an email per each new comment on one of your notebooks. This will not affect your moderation settings; e.g., a user such as yourself or Steven will have comments posted automatically and you will receive an email accordingly. That is, for this code to run more liberally, modify…[Read more]
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Sam White wrote a new post, Genome Assembly – Olympia oyster Redundans/Canu vs. Redundans/Racon, on the site Sam's Notebook 1 week, 6 days ago
Decided to compare the Redundans using Canu as reference and Redundans using Racon as reference. Both reference assemblies were just our PacBio data.Jupyter notebook (GitHub): <a […]
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Sam White wrote a new post, Genome Assembly – Olympia Oyster Redundans with Illumina + PacBio, on the site Sam's Notebook 2 weeks ago
Redundans should assemble both Illumina and PacBio data, so let’s do that.Sean had previously performed this – twice actually:
It wasn’t entirely clear how he had run Redundans the […]
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TL;DR – Redundans/Canu output file (scaffold.reduced.fa) is currently the best genome assembly.
However, the catch is that it’s missing a huge amount of data (the second set of mate-pair reads)…
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Sam White wrote a new post, Genome Assembly – minimap/miniasm/racon Overview, on the site Sam's Notebook 2 weeks, 1 day ago
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Sam White wrote a new post, Assembly Comparisons – Olympia oyster genome assemblies, on the site Sam's Notebook 2 weeks, 2 days ago
— UPDATE 20171009 —Having run through this a bunch of times now, I realized that the analysis below incorrectly identifies the outputs from Sean’s Redundans runs. The correct output from each of those runs […]
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Sam White wrote a new post, Samples Received – C.virginica gonad tissue from Katie Lotterhos, on the site Sam's Notebook 2 weeks, 2 days ago
Received and stored @-80C in rack 8, row 5, column 5.
The following information was sent with the samples:
Sample.ID
Date
Temp
pCO2
Notes031
26-Aug-2016
15
400032
26-Aug-2016
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Chris Hartgerink wrote a new post, Copyright and licenses in Open Access publishing, on the site Chris H.J. Hartgerink's Notebook 2 weeks, 2 days ago
tl;dr copyright restricts knowledge sharing and by extension production; the author can decide to empower knowledge sharing and production with specific Creative Commons licenses (i.e., only CC 0 or CC BY)
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Sam White wrote a new post, Goals – October 2017, on the site Sam's Notebook 2 weeks, 3 days ago
I guess one of my primary goals is to make sure I actually write my monthly goals each month.Is it bad that I’m writing goals about writing goals? Or, is it meta?
Regardless, I’m actually going to put a lot […]
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Sam White wrote a new post, DNA Isolation – Ava Withering Syndrome Transmission Study Tissues, on the site Sam's Notebook 3 weeks ago
Isolated DNA from 144 red abalone digestive gland tissue samples.
Tissue was weighed, minced with a razor blade, and transferred to 2mL snap cap tube containing 1mL of InhibtEX Buffer.
DNA was extracted using […]
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Pardon us, Sam,
This is our final test of new code which sends you an email per each new comment on one of your notebooks. This will not affect your moderation settings; e.g., a user such as yourself or Steven will have comments posted automatically and you will receive an email accordingly. That is, for this code to run more liberally, modify…[Read more]
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Sam White wrote a new post, DNA Isolation – Ava Withering Syndrome Transmission Study Tissues, on the site Sam's Notebook 3 weeks, 3 days ago
Isolated DNA from 58 red abalone digestive gland tissue samples.
Tissue was weighed, minced with a razor blade, and transferred to 2mL snap cap tube containing 1mL of InhibtEX Buffer.
DNA was extracted using the […]
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Sam White wrote a new post, DNA Isolation – Ava Withering Syndrome Transmission Study Tissues, on the site Sam's Notebook 4 weeks ago
Isolated DNA from 26 red abalone digestive gland tissue samples.
Tissue was weighed, minced with a razor blade, and transferred to 2mL snap cap tube containing 1mL of InhibtEX Buffer.
DNA was extracted using the […]
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Sam White wrote a new post, Genome Assembly – Olympia oyster PacBio minimap/miniasm/racon, on the site Sam's Notebook 1 month ago
In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.
I followed the pipeline described by this paper: <a […]
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Sam White wrote a new post, Genome Assembly – Olympia oyster PacBio minimap/miniasm/racon, on the site Sam's Notebook 1 month ago
In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.
I followed the pipeline described by this paper: <a […]
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