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 10, Summer 1
Description
SRP460750
Directory: /projects/tomato_genome/fnb/dataprocessing/SRP460750/nfcore-SL4-2024-05-21
Previously we noticed that SRA had mismatched some of the data incorrectly and 16 of the sample-names were mislabeled. Dr. Reid reached out and had SRA change everything to the correct sample names. Now we must rerun the muday SRA data again on the cluster with nextflow and make sure the data is correctly labeled.
For this task, we need to confirm and sanity-check the muday time course data that Rob recently uploaded and submitted to the Sequence Read Archive.
If the data are good, we will replace all the existing BAM, junctions, etc. files deployed in the "hotpollen" quickload site with newly processed data.
For this task:
Check SRP on NCBI and review submission
Download the data onto the cluster by using the SRP name
Run nf-core/rnaseq pipeline
Run our coverage graph and junctions scripts on the data
Note that all files should now use their "SRR" names instead of the existing file names.
Attachments
Issue Links
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- Closed
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