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
- relates to
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- Closed
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Activity
Branch: https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3739
Directory: /projects/tomato_genome/fnb/dataprocessing/SRP460750/nfcore-SL4-2024-05-21/results/star_salmon
Reviewer:
Check that files have reasonable sizes (no "zero" size files, for example)
Check that every "FJ.bed.gz" file has a corresponding "FJ.bed.gz.tbi" index file
Check that every bam file has a corresponding "FJ.bed.gz" file
Check that every bam file has a corresponding "scaled.bedgraph.gz" file
Check that every "scaled.bedgraph.gz" has a corresponding "scaled.bedgraph.gz.tbi"
I found 72
bam files (~ 400MB in size)
bai files (kb in size)
scaled.bedgraph.gz files (40MB in size)
more bedgraph tbi files (70k in size)
72 bed.gz files, 40MB in size
and 72 tbi files for these bad files
Looks like everything is here!
PR is merged. Ready for testing.
Review:
- All quick load files are accounted for in SL4 directory
- I made sure permission were accessible for group chmod -R g+w *
- The merged files on bitbucket are correct
Moving to Done!
Used this document to run the pipeline: https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit