November 21, 2024 18:47:09Daily Notes
Stuff that did not make the bar to postworthy
February 21, 2025
Why These Class Codes for lncRNA Discovery?****
- Intergenic lncRNAs (lincRNAs) → Class code “u”****
• They exist outside known protein-coding genes.
• Tend to be truly novel transcripts.
- Intronic lncRNAs → Class code “i”****
• These are found inside introns of known genes.
• Some intronic lncRNAs are functional and could be regulatory.
- Antisense lncRNAs → Class code “x”****
• Found on the opposite strand of known genes.
• Might regulate sense-strand transcription.
- Potential lncRNAs Overlapping Known Genes → Class code “o”****
• Need further filtering to ensure they are not protein-coding isoforms.
Research Notes: February 20, 2025
Today provided several valuable insights across multiple marine science domains:
From seminar, learned about novel approaches to enhancing resilience in commercially important species. Key points:
• Integration of multiple OMICS technologies (metabolomics, proteomics, transcriptomics) for comprehensive analysis
• Successful application in various species:
• Green-lipped mussels (summer mortality resistance)
• Pacific oysters (viral infection response)
• Chinook salmon (feed efficiency optimization)
• Geoduck cultivation
• Abalone heat wave resilienceParticularly interesting: The development of encapsulated feed technology for abalone, showing promising results in both land-based and open-water aquaculture systems.
Oyster Genetics Analysis
Data analysis session with Benjamin revealed interesting patterns:
• Observed distinct differences in copy number variance between diploid and triploid oysters
• Potential implications for stress response mechanisms
• New insights into gene loss patternsPhage Therapy Applications
Emerging therapeutic approach for aquaculture diseases:
• Discussion with Scripps collaborators highlighted potential applications for oyster pathogens
• Integration with existing disease management strategies
• Possibility for targeted bacterial control in aquaculture settingsFuture Directions
• Further investigation needed on specific genes involved in stress response
• Potential for combining phage therapy with resilience enhancement strategies
• Cross-disciplinary applications of OMICS technologies in aquacultureNote: Planning follow-up collaborative work with Scripps Institution of Oceanography to expand phage therapy research.
This synthesis of today’s learnings highlights the increasing convergence of molecular techniques, traditional aquaculture, and innovative therapeutic approaches in marine science. The integration of these methods could provide new solutions for industry challenges.
February 15, 2025
Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools found here: '/usr/bin/samtools'
Reference genome folder provided is ../data/ (absolute path is '/home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/data/)'
FastQ format assumed (by default)
Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4
Each Bowtie 2 instance is going to be run with 10 threads. Please monitor performance closely and tune down if necessary!
Input files to be analysed (in current folder '/home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/code'):
../data/22-Apul-meth/ACR-140-TP2_R1.fastp-trim.fq.gz
../data/22-Apul-meth/ACR-140-TP2_R2.fastp-trim.fq.gz
Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!)
Output will be written into the directory: /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/22-Apul-methylation/
Setting parallelization to single-threaded (default)
Summary of all aligner options: -q --score-min L,0,-1.0 -p 10 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Current working directory is: /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/code
Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/data/
Single-core mode: setting pid to 1
Paired-end alignments will be performed
=======================================
---
253164476 reads; of these:
253164476 (100.00%) were paired; of these:
252724097 (99.83%) aligned concordantly 0 times
215631 (0.09%) aligned concordantly exactly 1 time
224748 (0.09%) aligned concordantly >1 times
0.17% overall alignment rate
253164476 reads; of these:
253164476 (100.00%) were paired; of these:
252721074 (99.82%) aligned concordantly 0 times
210210 (0.08%) aligned concordantly exactly 1 time
233192 (0.09%) aligned concordantly >1 times
0.18% overall alignment rate
Processed 253164476 sequences in totalDecember 6, 2024.
OK didn’t do much analysis today but did decide that the next focus is going to be to take Chris nutation samples. We run them hopefully with the new next flow pipeline, but that’ll be ready to see if unit directional alignment fixes the odd CG ratio thing
Relavant Species info
Based on the differences in life history, ecology, and biology between Acropora pulchra, Pocillopora meandrina, and Pocillopora tuahiniensis, we would expect differences in their gene regulatory mechanisms. Here’s why: • Different Symbiotic Strategies and Environmental Sensitivity: The sources highlight that these species have distinct symbiotic strategies, with A. pulchra being a horizontal transmitter and both Pocillopora species being vertical transmitters. Additionally, A. pulchra is generally considered more sensitive to environmental change. These differences likely require distinct gene regulatory mechanisms to manage the acquisition, maintenance, and potential stress responses associated with their symbionts. ◦ A. pulchra needs to regulate genes involved in recognizing and incorporating symbionts from the environment, while the Pocillopora species need to regulate genes for the inheritance of symbionts. ◦ The higher environmental sensitivity of A. pulchra suggests that its gene regulatory mechanisms may be more responsive to environmental stressors, leading to differential gene expression patterns compared to the Pocillopora species. • Symbiont Community Composition: Each species associates with different dominant Symbiodiniaceae species and profiles. This variation in symbiont partners is likely to influence host gene expression, as different symbionts may produce different signaling molecules or metabolites that interact with host gene regulatory pathways. ◦ For example, the sources found that symbiont community composition was significantly related to host physiology in Porites. This suggests that the specific types of symbionts present can influence host gene expression patterns. • Cryptic Diversity and Holobiont Identity: The sources emphasize the presence of cryptic diversity within the Pocillopora genus and the importance of considering holobiont identity. Even within the same species, different host haplotypes can exhibit distinct physiological responses and associate with different symbiont communities. This suggests potential genetic differences in gene regulatory mechanisms between holobionts. • Physiological Differences: The sources detail significant physiological differences between these species, indicating that their gene regulatory mechanisms must be tuned to support their distinct physiological needs. ◦ For example, the sources note that Porites corals, with their thicker tissues, have higher overall physiological rates compared to Acropora and Pocillopora. This would necessitate differences in the regulation of genes involved in metabolic processes, growth, and calcification. • Morphological Differences: The sources describe differences in tissue structure, with Acropora and Porites having perforate tissues and Pocillopora having imperforate tissues. These morphological differences could influence the microenvironment experienced by the coral host and its symbionts, potentially leading to differences in gene expression patterns. ◦ For example, perforate tissues might allow for greater exchange of nutrients and gases, which could affect metabolic processes and the regulation of related genes. Overall, the sources provide strong evidence that the different life histories, ecologies, symbiont communities, and physiologies of Acropora pulchra, Pocillopora meandrina, and Pocillopora tuahiniensis are likely associated with differences in their gene regulatory mechanisms. Further research, specifically focusing on gene expression analysis across these species, would be needed to confirm and explore the specific nature of these differences.
quarto render
find . -name "*.qmd" -mtime -1 -exec quarto render {} \;Today in RStudio, I focused on several tasks related to my project “bestblogever.” I worked on rendering and saving files using Quarto for document preparation and management. I also engaged in coding activities, which included running shell scripts and managing directories and files for data processing. This involved setting up directories, creating checkpoint files, and running Bismark alignments, typically used for DNA methylation analysis. I ensured that the scripts executed successfully by checking command outputs and logging the results.
Additionally, I was involved in version control activities, such as staging, committing, and pushing changes to my Git repository. This included reviewing changes in various HTML and XML files related to my project documentation. I also managed my RStudio environment by loading workspaces and utilizing various RStudio features like the console, terminal, and background jobs.