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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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Rank | Ranked higher |
| Description | muday-2022-timeseries = SRP460750 |
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. |
| Summary | Rerun SRA muday 2022 timeseries data again with SL4 | Re-run SRA muday 2022 timeseries data again with SL4 |
| Sprint | Spring 10 [ 194 ] | Spring 10, Summer 1 [ 194, 195 ] |
| Rank | Ranked higher |
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"
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Molly Davis [ molly ] | Robert Reid [ robertreid ] |
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!
| Assignee | Robert Reid [ robertreid ] | Molly Davis [ molly ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Molly Davis [ molly ] | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
PR is merged. Ready for testing.
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Molly Davis [ molly ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
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!
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Used this document to run the pipeline: https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit