Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:5
-
Epic Link:
-
Sprint:Spring 4 2023 Feb 21
Description
Please review: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/Counts/ClusterCounts.Rmd
Glorias Requests:
1. PCA plots for all 3 genotypes at control and stress temperatures in each time point (so, this would be 4 PCA plots). Rob had sent graphs with all 4 time points, 3 genotypes and 2 temperatures and that was hard to parse out. Rasha showed her data with individual time points and it was much easier to follow.
2. I know that pipelines/analysis procedures evolve. Can you look at the analysis of DE genes with temperature within each genotype and make sure we have a final set of data. This is pertinent to compare with number 3! I think we decided that IQR 50 was the best metric
3. Analyses of DE genes between genotypes. We have not yet seen those genes for the current analysis pipeline and want to match those up with genes in Number 2. Since there are 3 genotypes, I guess the way this needs to be done is 3 pairwise comparisons at each temperature (so 6 comparisons), but if you all have thoughts on another way, we'd love to hear them.
4. Volcano plots with lines drawn at p values (not adjusted p-values) less than 0.05 and Log fold change (base 2) of 1.0. This would be comparing temperature response within genotypes (so 3 plots) and differences between genotypes at each temperature (so 6 plots).
5. We are excited to look at this data in IGB, so that is another thing we want to do and look at regions where there are DE genes.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Assignee | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description | Please review: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/Counts/ClusterCounts.Rmd |
| Attachment | Muday_SL5_RNAseq_Analysis.Rmd [ 17709 ] |
| Attachment | salmon.merged.gene_counts-SL5.tsv [ 17710 ] |
| Attachment | metafile.tsv [ 17711 ] |
| Attachment | metafile.tsv [ 17711 ] |
| Attachment | Muday_SL5_RNAseq_Analysis.Rmd [ 17709 ] |
| Attachment | salmon.merged.gene_counts-SL5.tsv [ 17710 ] |
Sorry, I should have been a little more clear!
Please add the files to a fork of https://bitbucket.org/hotpollen/flavonoid-rnaseq.
Also, when adding new data files, use the same prefix as previously created data files for the same data set.
Please carefully look over the contents of the "ExternalData" directory in https://bitbucket.org/hotpollen/flavonoid-rnaseq to understand where these new files fit in.
Thank you!
Also, please always include the ticket number in the commit message, following the existing pattern. This allows us to later on track down why a given change was made.
Update:
- Created Markdown:
Location: https://bitbucket.org/mdavis4290/analysis-flavonoid-rnaseq/src/main/RNAseq-Analysis/
Comments:
- I had to update the names for both files to match, here are the files I am using with the markdown:
Location: https://bitbucket.org/mdavis4290/analysis-flavonoid-rnaseq/src/main/RNAseq-Analysis/ - Might need to use 'cooksCutoff' and 'independentFiltering'
- Am I grouping factors correctly and adding the right factors together in the PCA plots?
[~RobertReid] Let me know what you think!
| Comment |
[ *Update:*
* Created Markdown: Location: https://bitbucket.org/mdavis4290/analysis-flavonoid-rnaseq/src/main/ Commit: https://bitbucket.org/mdavis4290/analysis-flavonoid-rnaseq/commits/07a47f479ce64d3e8ee51bebc92eca19cb434749 Comments: * I had to update the names for both files to match, here are the files I am using with the markdown: Location: https://bitbucket.org/mdavis4290/analysis-flavonoid-rnaseq/src/main/ * Might need to use 'cooksCutoff' and 'independentFiltering' * Am I grouping factors correctly and adding the right factors together in the PCA plots? [~RobertReid] Let me know what you think! ] |
| Comment | [ [~aloraine] Ok I created a repository for them here: https://bitbucket.org/mdavis4290/analysis-flavonoid-rnaseq/src/main/ ] |
[~aloraine] Ok I forked the repository and added commit. Here is the pull request:
https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/3
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Please see change requests attached to the PR, repeated here, as well:
Change requests:
Please do all new work on a branch named for the ticket. Commit to your branch, not main. This is called a “fork and branch workflow”. Take your time to review how this works. Here’s a tutorial that explains it: Forking Workflow Atlassian Git Tutorial
Rename data files and metadata files so that they include this prefix in the name: muday-144-SL5, as was done for the multiqc reports in ExternalDataSets folder.
Include the ticket number in every commit. See examples in the commit history for the repository.
Please rename the folder “muday-144-analysis” to distinguish it from other data sets analyzed in this same repository.
Please rename your new Markdown file “muday-144-SL5-Clusters.Rmd”
In addition to adding the Markdown, knit the Markdown and add the knitted “html” version.
Once all this is done, I’ll fetch your branch and try to run your code.
| Description | Please review: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/Counts/ClusterCounts.Rmd |
Please review: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/Counts/ClusterCounts.Rmd
1. PCA plots for all 3 genotypes at control and stress temperatures in each time point (so, this would be 4 PCA plots). Rob had sent graphs with all 4 time points, 3 genotypes and 2 temperatures and that was hard to parse out. Rasha showed her data with individual time points and it was much easier to follow. 2. I know that pipelines/analysis procedures evolve. Can you look at the analysis of DE genes with temperature within each genotype and make sure we have a final set of data. This is pertinent to compare with number 3! I think we decided that IQR 50 was the best metric 3. Analyses of DE genes between genotypes. We have not yet seen those genes for the current analysis pipeline and want to match those up with genes in Number 2. Since there are 3 genotypes, I guess the way this needs to be done is 3 pairwise comparisons at each temperature (so 6 comparisons), but if you all have thoughts on another way, we'd love to hear them. 4. Volcano plots with lines drawn at p values (not adjusted p-values) less than 0.05 and Log fold change (base 2) of 1.0. This would be comparing temperature response within genotypes (so 3 plots) and differences between genotypes at each temperature (so 6 plots). 5. We are excited to look at this data in IGB, so that is another thing we want to do and look at regions where there are DE genes. |
| Description |
Please review: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/Counts/ClusterCounts.Rmd
1. PCA plots for all 3 genotypes at control and stress temperatures in each time point (so, this would be 4 PCA plots). Rob had sent graphs with all 4 time points, 3 genotypes and 2 temperatures and that was hard to parse out. Rasha showed her data with individual time points and it was much easier to follow. 2. I know that pipelines/analysis procedures evolve. Can you look at the analysis of DE genes with temperature within each genotype and make sure we have a final set of data. This is pertinent to compare with number 3! I think we decided that IQR 50 was the best metric 3. Analyses of DE genes between genotypes. We have not yet seen those genes for the current analysis pipeline and want to match those up with genes in Number 2. Since there are 3 genotypes, I guess the way this needs to be done is 3 pairwise comparisons at each temperature (so 6 comparisons), but if you all have thoughts on another way, we'd love to hear them. 4. Volcano plots with lines drawn at p values (not adjusted p-values) less than 0.05 and Log fold change (base 2) of 1.0. This would be comparing temperature response within genotypes (so 3 plots) and differences between genotypes at each temperature (so 6 plots). 5. We are excited to look at this data in IGB, so that is another thing we want to do and look at regions where there are DE genes. |
Please review: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/Counts/ClusterCounts.Rmd
Glorias Requests: 1. PCA plots for all 3 genotypes at control and stress temperatures in each time point (so, this would be 4 PCA plots). Rob had sent graphs with all 4 time points, 3 genotypes and 2 temperatures and that was hard to parse out. Rasha showed her data with individual time points and it was much easier to follow. 2. I know that pipelines/analysis procedures evolve. Can you look at the analysis of DE genes with temperature within each genotype and make sure we have a final set of data. This is pertinent to compare with number 3! I think we decided that IQR 50 was the best metric 3. Analyses of DE genes between genotypes. We have not yet seen those genes for the current analysis pipeline and want to match those up with genes in Number 2. Since there are 3 genotypes, I guess the way this needs to be done is 3 pairwise comparisons at each temperature (so 6 comparisons), but if you all have thoughts on another way, we'd love to hear them. 4. Volcano plots with lines drawn at p values (not adjusted p-values) less than 0.05 and Log fold change (base 2) of 1.0. This would be comparing temperature response within genotypes (so 3 plots) and differences between genotypes at each temperature (so 6 plots). 5. We are excited to look at this data in IGB, so that is another thing we want to do and look at regions where there are DE genes. |
| Story Points | 2 | 5 |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Request for [~molly]:
Please use bitbucket to share files instead of attaching to the tickets. Fork the repository, make a branch, add the new files to it, and add a link to the branch to the ticket. We can then look at the new files by following the link.
The problem with attaching so many files to these tickets is that it uses up a lot of extra disk space on our server, making maintenance more difficult and expensive.