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:2
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Epic Link:
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Sprint:Spring 7, Spring 8, Spring 9, Spring 10
Description
Data has been submitted to SRA and now needs to be reviewed. To do this we perform a rerun of the data by pulling it from SRA directly and pushing it through the nextflow pipeline and prepping it for IGB quick load. To confirm that the data on SRA is correct we can make a few comparisons with the original data.
- Compare files sizes of the original data to the new rerun file sizes.
- Open IGB and compare bam and coverage graphs with the original and rerun data.
- Perform these comparisons SL4 and SL5
mark-2022-timeseries cluster Directories:
Original: /projects/tomato_genome/fnb/dataprocessing/mark-2022-timeseries
Re-run: /projects/tomato_genome/fnb/dataprocessing/SRP441343
Attachments
Issue Links
Activity
Added a new line of code for the CheckSRA markdowns so that if the output file is empty is will not save. I am going to commit the changes for this markdown and the other markdowns as well for muday lab CheckSRA in ticket IGBF-3693
if(nrow(output_df) > 0) readr::write_csv(output_df, output_fname)
I reviewed the new text of the Markdown using the bitbucket interface. It looks like the code and text about the code is no longer referencing the Muday dataset but is instead only talking about the current task, which is making sure that the pre- and post-SRA submission data are cool.
Please submit PR when ready.
attn: Molly Davis
PR is merged. Moving to DONE.
Use this script 72_F3H_PollenTube/CheckSRA.Rmd and adapt it to work with Mark's data.