Sam’s Notebook

University of Washington - Fishery Sciences - Roberts Lab

Posts - Page 2 of 137

RNA Isolation - O.nerka Berdahl Tissues

  • 3 min read

Finally got around to tackling this GitHub issue regarding isolating RNA from some Oncorhynchus nerka (sockeye salmon) tissues we have from Andrew Berdahl’s lab (a UW SAFS professor) to use for RNAseq and/or qPCR. We have blood, brain, gonad, and liver samples from individual salmon from two different groups: territorial and social individuals. We’ve decided to isolate RNA from brain, gonads, and liver from two individuals within each group. All samples are preserved in RNAlater and stored @ -80oC.

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Data Wrangling - C.virginica NCBI GCF_002022765.2 GFF to Gene BED File

  • 1 min read

When working to identify differentially expressed transcripts (DETs) and genes (DEGs) for our Crassostrea virginica (Eastern oyster) RNAseq/DNA methylation comparison of changes across sex and ocean acidification conditions (https://github.com/epigeneticstoocean/2018_L18-adult-methylation), I realized that the DEG tables I was generating had excessive gene counts due to the fact that the analysis (and, in turn, the genome coordinates), were tied to transcripts. Thus, genes were counted multiple times due to the existence of multiple transcripts for a given gene, and the analysis didn’t list gene coordinate data - only transcript coordinates.

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Differential Transcript Expression - C.virginica Gonad RNAseq Using Ballgown

  • 1 min read

In preparation for differential transcript analysis, I previously ran our RNAseq data through StringTie on 20210726 to identify and quantify transcripts. Identification of differentially expressed transcripts (DETs) and genes (DEGs) will be performed using ballgown. This notebook entry will be different than most others, as this notebook entry will simply serve as a “landing page” to access/review the analysis; as the analysis will evolve over time and won’t exist as a single computing job with a definitive endpoint.

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Assembly Indexing - C.bairdi Transcriptome cbai_transcriptome_v3.1.fasta with Hisat2 on Mox

  • 2 min read

We recently received reviews back for the Tanner crab paper submission (“Characterization of the gene repertoire and environmentally driven expression patterns in Tanner crab (Chionoecetes bairdi)”) and one of the reviewers requested a more in-depth analysis. As part of addressing this, we’ve decided to identify SNPs withing the _Chionoecetes bairdi (Tanner crab) transcriptome used in the paper (cbai_transcriptome_v3.1). Since the process involves aligning sequencing reads to the transcriptome, the first thing that needed to be done was to generate index files for the aligner (HISAT2, in this particular case), so I ran HISAT2 on Mox.

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Computer Management - Disable Sleep and Hibernation on Raven

  • ~1 min read

We’ve been having an issue with our computer Raven where it would become inaccessible after some time after a reboot. Attempts to remote in would just indicate no route to host or something like that. We realized it seemed like this was caused by a power saving setting, but changing the sleep setting in the Ubuntu GUI menu didn’t fix the issue. It also seemd like the sleep/hibernate issue was only a problem after the computer had been rebooted and no one had logged in yet…

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