Site-Wide Activity

Sam White wrote a new post, Library Construction – Geoduck Water Filter Metagenome with Nextera DNA Flex Kit (Illumina), on the site Sam's Notebook 2 weeks, 3 days ago
Made Illumina libraries with goeduck metagenome water filter DNA I previously isolated on:
- 20180411
- 20180426
We used a free Nextera DNA Flex Kit (Illumina) that we won in a contest held by Illumina!

Followed […]
Sam White wrote a new post, BS-seq Mapping – Olympia oyster bisulfite sequencing: Bismark Continued, on the site Sam's Notebook 3 weeks, 3 days ago

Previously took the analysis just through the mapping, but didn’t realize Steven wanted me to fully process the data.

So, as en exercise, I followed through with deduplication and sorting of the BAM files.

Then, […]
Sam White wrote a new post, Transposable Element Mapping – Crassostrea virginica NCBI Genome Assembly using RepeatMasker 4.07, on the site Sam's Notebook 3 weeks, 4 days ago

Genome used: NCBI GCA_002022765.4_C_virginica-3.0

I ran RepeatMasker (v4.07) with RepBase-20170127 and RMBlast 2.6.0 with species set to Crassotrea virginica.

All commands were documented in a Jupyter Notebook […]
Sam White wrote a new post, Transposable Element Mapping – Olympia Oyster Genome Assembly using RepeatMasker 4.07, on the site Sam's Notebook 1 month ago

Steven wanted transposable elements (TEs) in the Olympia oyster genome identified.

After some minor struggles, I was able to get RepeatMasker installed on on both of our Apple Xserves (emu & roadrunner; running […]
Sam White wrote a new post, DNA Received – Sea lice DNA from Cris Gallardo-Escarate at Universidad de Concepción , on the site Sam's Notebook 1 month ago
Received Caligus tape DNA – two samples:
- Female 1 .
- Female 2 .
Stored in slots H4 and H5 in “Sam’s gDNA Box #2″ in the FTR 213 -20oC freezer.

Google Sheet: Sam’s gDNA Box #2
Sam White wrote a new post, Software Installation – RepeatMasker v4.0.7 on Emu/Roadrunner Continued, on the site Sam's Notebook 1 month ago

After yesterday’s difficulties getting RMblast to compile, I deleted the folder and went through the build process again.

This time it worked, but it did not put rmblastn in the specified location […]
Sam White wrote a new post, Software Installation – RepeatMasker v4.0.7 on Emu/Roadrunner, on the site Sam's Notebook 1 month ago

Steven asked that I re-run some Olympia oyster transposable elements analysis using RepeatMasker and a newer version of our Olympia oyster genome assembly.

Installed the software on both of the Apple Xserves (Emu […]
Sam White wrote a new post, TrimGalore/FastQC/MultiQC – TrimGalore! RRBS Geoduck BS-seq FASTQ data (directional), on the site Sam's Notebook 1 month, 1 week ago

Earlier this week, I ran TrimGalore!, but set the trimming, incorrectly – due to a copy/paste mistake, as --non-directional, so I re-ran with the correct settings.

Steven requested that I trim the Geoduck RRBS […]
Sam White wrote a new post, FastQC – RRBS Geoduck BS-seq FASTQ data, on the site Sam's Notebook 1 month, 1 week ago

Earlier today I finished trimming Hollie’s RRBS BS-seq FastQ data.

However, the original files were never analyzed with FastQC, so I ran it on the original files.

These libraries were originally created by […]
Sam White wrote a new post, TrimGalore/FastQC/MultiQC – TrimGalore! RRBS Geoduck BS-seq FASTQ data, on the site Sam's Notebook 1 month, 1 week ago

20180516 – UPDATE!!

THIS WAS RUN WITH THE INCORRECT SETTING IN TRIMGALORE! --non-directional

WILL RE-RUN

Steven requested that I trim the Geoduck RRBS libraries that we have, in preparation to run them […]
Sam White wrote a new post, Data Management – Illumina NovaSeq Geoduck Genome Sequencing, on the site Sam's Notebook 1 month, 1 week ago

As part of the Illumina collaborative geoduck genome sequencing project, their end goal has always been to sequence the genome in a single run.

They’ve finally attempted this by running 10x Genomics, Hi-C, […]
Sam White wrote a new post, Assembly – Geoduck Hi-C Assembly Subsetting, on the site Sam's Notebook 1 month, 1 week ago
Steven asked me to create a couple of subsets of our Phase Genomics Hi-C geoduck genome assembly (pga_02):
- Contigs 10kbp
- Contigs 30kbp
I used pyfaidx on Roadrunner and the following commands:
```
faidx […]
```
Sam White wrote a new post, Read Mapping – Mapping Illumina Data to Geoduck Genome Assemblies with Bowtie2, on the site Sam's Notebook 1 month, 2 weeks ago

We have an upcoming meeting with Illumina to discuss how the geoduck genome project is coming along and to decide how we want to proceed.

So, we wanted to get a quick idea of how well our geoduck assemblies are […]
Sam White wrote a new post, BS-seq Mapping – Olympia oyster bisulfite sequencing: TrimGalore > FastQC > Bismark, on the site Sam's Notebook 1 month, 2 weeks ago
Steven asked me to evaluate our methylation sequencing data sets for Olympia oyster.

According to our Olympia oyster genome wiki, we have the following two sets of BS-seq data:
- Whole genome BS-seq (2015)
- MBD […]
Sam White wrote a new post, Assembly & Stats – SparseAssembler (k95) on Geoduck Sequence Data > Quast for Stats, on the site Sam's Notebook 1 month, 3 weeks ago

Had a successful assembly with SparseAssembler k101, but figured I’d just tweak the kmer setting and throw it in the queue and see how it compares; minimal effort/time needed.

Initiatied an assembly run using <a […]
Sam White wrote a new post, Assembly Stats – Geoduck Genome Assembly Comparisons w/Quast – SparseAssembler, SuperNova, Hi-C, on the site Sam's Notebook 1 month, 3 weeks ago
Steven requested a comparison of geoduck genome assemblies.

Ran the following Quast command:
```
/home/sam/software/quast-4.5/quast.py 
-t 24 
--labels […]
```
Sam White wrote a new post, Assembly Stats – Geoduck Hi-C Assembly Comparison, on the site Sam's Notebook 1 month, 3 weeks ago
Ran the following Quast command to compare the two geoduck assemblies provided to us by Phase Genomics:
```
/home/sam/software/quast-4.5/quast.py 
-t 24 
--labels 20180403_pga,20180421_pga […]
```
Sam White wrote a new post, DNA Isolation & Quantification – Metagenomics Water Filters, on the site Sam's Notebook 1 month, 4 weeks ago

After discussing the preliminary DNA isolation attemp with Steven & Emma, we decided to proceed with DNA isolations on the remaining 0.22μm filters.

Isolated DNA from the following five filters:

DNA was […]
Sam White wrote a new post, Total Alkalinity Calculations – Yaamini’s Ocean Chemistry Samples, on the site Sam's Notebook 2 months ago

I ran a subset of Yaamini’s ocean chemistry samples on our T5 Excellence titrator (Mettler Toledo) at the beginning of April. The subset were samples taken from the beginning, middle, and end of the experiment. […]
Sam White wrote a new post, Assembly – SparseAssembler (k 111) on Geoduck Sequence Data, on the site Sam's Notebook 2 months ago

Continuing to try to find the best kmer setting to work with SparseAssemlber after the last attempt failed due to a kmer size that was too large (k 131; which happens to be outside the max kmer size [127] for […]
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