Posts
SNP Identification - C.bairdi Day 2 DEG Pooled Samples Using bcftools on Mox
RNAseq Alignments - C.bairdi Day 2 Infected-Uninfected Temperature Increase-Decrease RNAseq to cbai_transcriptome_v3.1.fasta with Hisat2 on Mox
Ealier today, I created the necessary Hisat2 index files for cbai_transcriptome_v3.1. Next, I needed to actually get the alignments run. The alignments were performed using HISAT2 on Mox using the following set of trimmed FastQ files from 2020414:
Assembly Indexing - C.bairdi Transcriptome cbai_transcriptome_v3.1.fasta with Hisat2 on Mox
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.
Computer Servicing - APC SUA2200RM2U UPS Battery Replacement
Replaced the battery pack in the top APC SUA2200RM2U UPS in our computing “cluster” cabinet.
Computer Management - Disable Sleep and Hibernation on Raven
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…
Genome Annotations - Splice Site and Exon Extractions for C.virginica GCF_002022765.2 Genome Using Hisat2 on Mox
Previously performed quality trimming on the Crassostrea virginica (Eastern oyster) gonad/sperm RNAseq data on 20210714. Next, I needed to identify exons and splice sites, as well as generate a genome index using HISAT2 to be used with StringTie downstream to identify potential alternative transcripts. This utilized the following NCBI genome files:
RNAseq Alignments - C.virginica Gonad Data to GCF_002022765.2 Genome Using StringTie on Mox
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.
Trimming - C.virginica Gonad RNAseq with FastP on Mox
Needed to trim the Crassostrea virginica (Eastern oyster) gonad RNAseq data we received on 20210528.
Summary - Geoduck RNAseq Data
Per this GitHub Issue, I’ve compiled a summary table, with links, of all of our Panopea generosa (Pacific geoduck) RNAseq data as it exists in NCBI. This will be a “dynamic” notebook entry, whereby I will update this post continually as we acquire new data and/or change the information we’d like to have here.
Genome Analysis - Identification of Potential Contaminating Sequences in Panopea-generosa-v1.0 Assembly Using BlobToolKit on Mox
As part of our Panopea generosa (Pacific geoduck) genome sequencing efforts, Steven came across a tool designed to help identify if there are any contaminating sequences in your assembly. The software is BlobToolKit. The software is actually a complex pipeline of separate tools ([minimap2])https://github.com/lh3/minimap2, BLAST, DIAMOND BLAST, and BUSCO) which aligns sequencing reads and assigns taxonomy to the reads, as well as marking regions of the assembly with various taxonomic assignments.