Sam’s Notebook

University of Washington - Fishery Sciences - Roberts Lab


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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RNAseq Alignments - C.virginica Gonad Data to GCF_002022765.2 Genome Using StringTie on Mox

  • 11 min read

As part of identifying alternative transcripts in the Crassostrea virginica (Eastern oyster) gonad RNAseq data we have, I previously used HISAT2 to index the NCBI Crassostrea virginica (Eastern oyster) genome and identify exon/splice sites on 20210720. Then, I used this genome index to run StringTie on Mox in order to map sequencing reads to the genome/alternative isoforms.

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