Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:0.5
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Epic Link:
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Sprint:Summer 7 2023 Aug 7, Summer 8 2023 Aug 21
Description
File: muday-144-SL5_counts-salmon.txt
Request email:
Also, we have a small problem with the excel files on the DE genes within genotype and between treatments, that I think you can help us with easily.
We are trying to run an enrichment analysis and the software does not recognize the newest V5 genome. You gave us the S4 IDs, but they are part of the description, rather than a separate column. Is there a way to add this to the spreadsheet as a column? That way we can cut and paste a group without manually extracting each gene ID from that text heavy gene description list.
Thanks
Gloria
Attachments
Activity
References / Documentation:
This makes gene descriptions, using input from SL4_SL5_description.R.
Possible improvement:
- Modify the "DescriptionMapping" code to create SL4_SL5_description_tomato.csv (new file)
- Make new repo to capture just the description mapping code, and make it a "product" for bioinformatics researchers like us
Possible improvements:
- Modify "AddGeneAnnotations.Rmd" so that it adds a new column "SL4_gene_id"
Possible benefit of above: Fewer files to track
Reviewer:
- Please check code for any running errors or output errors. Also if I need to clean anything up!
- Check the output files and see if the structure is correct and makes sense based on Dr. Muday's request.
Thank you!
Dr. Muday asked for the SL4 gene names to be their own column with the description. So I made an R script and created an output file with the columns "SL4, SL5, Description". I also just added the new SL4 column to the original counts file.
Script:
SL4_SL5_Description.R
File with just gene names and description:
SL4_SL5_description_tomato.csv
File with SL4 column added on to the end of original counts file:
SL4_SL5_counts_muday-144.csv
Re-reading above, I realized that my previous comments sounded too much like commands for my taste, and not enough like suggestions. I revised them.