Created new branch with updates. Merged into main in team repo.

Molly - just letting you know that the new code addressing sample switching is merged into the main branch. Please take a look. If you do not observe anything that need to be changed, please move this ticket to DONE. If you do see a problem, make a note of it and move this ticket back to "To-Do"

Thank you!!

attn: [~molly]

Update:

Muday lab tracked down the problem that caused the sample switching. It was due to misunderstanding on the sequencing facility side. See attached PDF.

Re-opening the ticket.

During scrum, decided to make copies of the original misnamed fastq files using new names that match what the samples truly are.
Ann: I would like to use our sample codes in the names.

I'd like to look into how the information shown on SRA record pages corresponds to columns in the sample submission table.

Motivation:

• Will help pick great values for each column that illuminate the experimental design.
• Will help Johnson lab members, students, etc. re-use these data for stuff

Azenta sample pictures with labels.pptx Muday lab RNA samples for sample name conversion.xls

These are the 2 files shared by Gloria after they resolved the sample switching by the sequencing company.

Gloria's email blurb:
"Anthony and I separated worked through the misordered samples and both came up with the same pattern. In the attached Excel sheet, you can see in the FIRST column what your original sample names were (before that short switch of are). In the SECOND column are what those samples already are.

When you rename the samples, we'd like you to keep the old name on the sheet someone to present in any confusion. What would be really helpful to us is if after you rename the lanes, you could put them in the intended order.

We are mining this data to look at the transcription of specific genes. Ann did note that we should look at normalized reads. We'd love to have such a spreadsheet that had the normalized reads. We'd also love this exported to an excel sheet with the SolyIDs of each gene and the gene names.

Now that we have clear sample identities, we'd love to see if the PCA plot shows groups based on temperature and genotypes!"

New email from Muday lab with attachments Excel spreadsheet with new file name mappings and PowerPoint with images of the original sample boxes are now added to the repository.

See flavonoid-rnaseq/muday-144-analysis/Documentation.

Modifying code now.

Updated the UNC Charlotte HPC cluster to reflect the changes in sample names.

Sample names are being left in the original form. This is for the raw sequence data backed up on cluster at:

/projects/tomato_genome/rnaseq/muday144-timeSeries-checkReadMEFIRST

I changed the folder name to suggest that one should check out the README !!
And in the folder I added the README.txt.

Within the README.txt I mention what has happened and then point the user to the EXCEL file the highlights the sample name switching that is in bitBucket HotPollen.

https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/muday-144-analysis/Documentation/Muday-lab-RNA-samples-for-sample-name-conversion.xlsx

Updated AddGeneAnnotations.Rmd to incorporate NEW sample renaming scheme recommended by Muday lab in

• flavonoid-rnaseq/72_F3H_PollenTube/Documentation/Muday-lab-RNA-samples-for-sample-name-conversion.xlsx

To review:

• Read the knitted Markdowns AddGeneAnnotations.pdf and MakeMdsPlots.pdf
• Check output file sample_renaming_summary.txt. Compare to Muday-lab-RNA-samples-for-sample-name-conversion.xlsx.

Note that the new code and new files are already committed to the main branch of the team repository.

Gene annotations and Mds plots look like they have accurate renaming for samples provided by Muday lab. I compared the renaming summary to the naming conversions and they seem to match each other. Let me know if you would like to make a new ticket to perform the DESeq analysis with the new renamed counts file muday-144-SL5_counts-salmon.txt.

Ann Loraine

No, instead make a ticket tracking notifying Muday Lab of the good news.

Updating makeAnnotsXml.py to use the new labels.

Committed new annots.xml file and new script version to repository