31 January 2024
Wednesday
- More debugging of P.evermanni RNAseq abundance quantification. (See Github issues and notebook post for details)
30 January 2024
Tuesday
- class/classwork (prep and leading FISH510 discussion)
- Consolidated a bunch of cool ideas/questions fro future reading/projects here, will make this my go-to document for recording this stuff (so I don’t just forget it all!)
- my fix for reformatting the converted gff -> fasta file for P.evermani kallisto indexing is not working, due to a mysterious issue with fastx_collapser – details in github issue
- Finished running P.meandrina kallisto (code here, output matrix here).
29 January 2024
Monday
Class and classwork
P.evermanni kallisto work – think I figured out how to convert gff to fasta and reformat appropriately for kallisto indexing (bedtools getFasta, fastx_toolkit fasta_formatter, fastx_toolkit fastx_collapser)
26 January 2024
Friday
25 January 2024
Thursday
Finished running A.pulchra kallisto (code here, output matrix here). I did see that there’s already a count matrix for A.pulchra linked in the deep dive repo (here), but it’s different to my kallisto output – maybe run using different reference? Isn’t entirely clear, but I think that may be from the lncRNA work, which was using genome reference through HiSat?
Also started on process for P.evermanni, but realized that reference data is only available as a CDS gff file, not as a FASTA, and kallisto requires FASTA format to generate an index. I think I’ll ask about it at Science Hour tomorrow
24 January 2024
Wednesday
got going on A.pulchra gene expression work, working out kinks of finding/downloading trimmed RNAseq reads and appropriate transcripts reference, and running through kallisto
listened to this week’s chapter for DEI meeting tomorrow
23 January 2024
Tuesday
class and classwork – Megan and I are picking papers for our FISH510 meeting next week that’s focused on epigenetics!
looked through cod RNA extraction QC report and revised selection of samples for methylation work. Only tissue samples that a) are being RNAseq’d; b) have sufficient RNA quantity; and c) have RIN values >6 were considered
22 January 2024
Monday
Finally got access to TREQ!
Classwork
finished high-level summary of smRNA ID workflow for E5 deep dive manuscript
Proposal writing class – we watched an example of an animated video over-viewing a lab’s work w/ microplastics in a very general-public-friendly way, it was sick! That would be a really cool component to create for the lab or for a future project/grant/proposal
19 January 2024
Friday
Read some papers for FISH510 – one of them, Császár et al. 2010 (adaptive potential of a set of coral and symbiont stress response traits) got me wondering about what DGE analysis work has been done on the symbionts separately from the host?
Discussion write up for FISH510
prelim work on cod DGE paper
18 January 2024
Thursday
Lab meeting – Chris made a really awesome, helpful comment about remembering to enjoy the process of work/grad school, and Grace mentioned she’s using a new method to improve her productivity/focus by specifically allocating timed sections of work time and downtime (e.g. 25min working straight through, then 5 min for standing up, walking aruond, anything non-work related) that I think I’m going to try!
Ariana suggested assembling de novo transcriptome from our rnaseq data, which I know is a thing but I still don’t really get it…? How can you get useful/trustworthy information by comparing your data to itsself…?
^in effort to make sense of above question I made a quick sketch – I think it’s something like this? I realized that I forgot (for the nth time) that I’m working with RNA now, not DNA, so there are multiple copies of every sequenced transcript, and for DGE work the relative abundances of the transcripts, rather than presence/absence, is what matters.
Feeling very dumb and confused about the minutia of how to do the deep dive gene expression stuff so switched back to a generic DGE pipeline in preparation for the cod samples. Going to use Megan’s clam data (see full discussion of her workhere) as test data to push through my workflow.
17 January 2024
Wednesday
After talking w Zach I think I have an idea of how to start writing up a condensed version of the sRNA methods for the deep dive ncRNA manuscript.
Also, Zach and I talked about how to move forward with gene expression analysis for the E5 deep dive. We have trimmed RNAseq reads for the three species but we couldn’t find any published transcriptomes. However, for P.meandrina we found NCBI published gff files with only annotated protein-coding genes, which could maybe be used to approximate a transcriptome file? We’re not sure if that work correctly with kallisto though, or if we’d still need to use HiSat…
Read up on some of the sncRNA tools we used to write up on them in the deep dive manuscript (loving how it takes like 40min of reading to write 1 summary sentence of how something works).
16 January 2024
Tuesday
Continued compiling/modifying/writing code for a general RNAseq analysis pipeline for use in the cod and/or E5 projects. Will be meeting w/ Zach tomorrow to talk about E5 molecular stuff (writing and gene expression analysis)
Class
Did some work on updating CV
15 January 2024
Monday
Classwork + papers
12 January 2024
Friday
E5 Molecular group meeting (notes here)
Classwork
11 January 2024
Thursday
eScience Institute Data Carpentry workshop, Day 4
10 January 2024
Wednesday
eScience Institute Data Carpentry workshop, Day 3
Finished review of TTS tools – I think I’m going to go with Speechify
09 January 2024
Tuesday
eScience Institute Data Carpentry workshop, Day 2
Classes, finished transcribing SICB notes
08 January 2024
Monday
eScience Institute Data Carpentry workshop, Day 1
First day of classes for the Winter quarter
06 January 2024
Saturday
05 January 2024
Friday
Cnidarian Social after the conference – super fun!
Talked w Steven about next steps of coral stuff – move towards combining sRNA and RNAseq stuff to examine how the sRNAs are involved in genome expression
04 January 2024
Thursday
03 January 2024
Wednesday
02 January 2024
Tuesday
MISS Grant Writing Workshop (notes here)
MISS Figures and Illustrations Workshop
01 January 2024
Monday
Did some Lab Notebook work – set up new section for miscellaneous posts, set some January goals, and set up my January daily post page (which you’re currently reading)
Went through the (many, many) talks/events at SICB for the first few days and planned out my itinerary
Started writing up my review of different TTS services – find details here