Notes: From looking at [~RobertReid] meta data file it seems that replication 1 is pollinated pistils and replication 2 in unpollinated pistils for the 2021 data.

Dr. Reid's MetaData file: https://docs.google.com/spreadsheets/d/1qvZzKeLc3S28ceE03_uuzOXn6vaE2oM8/edit#gid=471813138

Request: Can someone please confirm that 2021 data rep 1 samples are pollinated and rep 2 samples are unpollinated?

"Request: Can someone please confirm that 2021 data rep 1 samples are pollinated and rep 2 samples are unpollinated?"

I believe that is correct! It was a very small sequencing run to test the whole process out.

In this sequence sample sheet:

https://docs.google.com/spreadsheets/d/1WwPzifPzbACmgS3uR_V92cYIGN3qS1yWPGHBu7DY_-I/edit?usp=sharing

it is confirmed. That what they call R1 is the "pistils"
and the R2 is the "unpollinated pistil".

This is confusing of course because we also have R1 and R2 referring to the paired end sequence files also.

When we look at all the files from this dataset:
Tamaulipas-pistils-0hr-25C-R1_R1_001.fastq.gz Tamaulipas-pistils-3hr-25C-R1_R2_001.fastq.gz Tamaulipas-pistils-3hr-37C-R2_R1_001.fastq.gz Tamaulipas-pistils-8hr-25C-R2_R2_001.fastq.gz
Tamaulipas-pistils-0hr-25C-R1_R2_001.fastq.gz Tamaulipas-pistils-3hr-25C-R2_R1_001.fastq.gz Tamaulipas-pistils-3hr-37C-R2_R2_001.fastq.gz Tamaulipas-pistils-8hr-37C-R1_R1_001.fastq.gz
Tamaulipas-pistils-0hr-25C-R2_R1_001.fastq.gz Tamaulipas-pistils-3hr-25C-R2_R2_001.fastq.gz Tamaulipas-pistils-8hr-25C-R1_R1_001.fastq.gz Tamaulipas-pistils-8hr-37C-R1_R2_001.fastq.gz
Tamaulipas-pistils-0hr-25C-R2_R2_001.fastq.gz Tamaulipas-pistils-3hr-37C-R1_R1_001.fastq.gz Tamaulipas-pistils-8hr-25C-R1_R2_001.fastq.gz Tamaulipas-pistils-8hr-37C-R2_R1_001.fastq.gz
Tamaulipas-pistils-3hr-25C-R1_R1_001.fastq.gz Tamaulipas-pistils-3hr-37C-R1_R2_001.fastq.gz Tamaulipas-pistils-8hr-25C-R2_R1_001.fastq.gz Tamaulipas-pistils-8hr-37C-R2_R2_001.fastq.gz

It is a mess!! But that is ok. It is workable.
The FIRST R1/R2 refers to the sample number. the 2ND refers to pair 1/2 of the sequence file.

Change request:

Please use the term "pistil" (singular) instead of "pistils" (plural) when referring to sample type.

Note: I need to change the replication numbers to dashes or blanks because there are no replications in this experiment.

Branch: https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3377

Notes: I went ahead and made sure that the 2021 and 2023 experiments/data were in their own sample sheets due to them being different experiments.

My apologies to [~molly].

I already renamed KP_sample_sheet.xlsx to KP_sample_sheet_2023.xlsx. I also made a few changes to the spreadsheet that I would like to keep.

So, rather than use your commit on this branch by merging and then resolving the conflict that will result from the editing and renaming work we both did on KP_sample_sheet.xlsx, I'm going to add your new file Ravi_Sample_sheet_2021.xlsx directly to main, thus skipping the PR step for this task. I am also going to keep my edits to KP_sample_sheet.xlsx, which I also renamed KP_sample_sheet_2003.xlsx.

add new commit to main: 1fe9319 with message "IGBF-3377 Track 2021 samples from Ravi Palanivelu lab"

Moving to Done.