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 2, Summer 1, Summer 2
Description
Experiment name is 30-681594536. SRP486761
Directory: /projects/tomato_genome/fnb/dataprocessing/SRP486761
For SL4 and SL5.
For this task, we need to confirm and sanity-check the Ravi 30-681594536 data that Rob 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
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Sprint | Spring 2 [ 186 ] | Spring 2, Spring 3 [ 186, 187 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Spring 2, Spring 3 [ 186, 187 ] | Spring 2 [ 186 ] |
| Description |
Experiment name is 30-681594536. Still waiting for {color:#d04437}SRP number{color}.
For SL4 and SL5. For this task, we need to confirm and sanity-check the Ravi 30-681594536 data that Rob 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. |
Experiment name is 30-681594536. SRP486761
For SL4 and SL5. For this task, we need to confirm and sanity-check the Ravi 30-681594536 data that Rob 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. |
| Sprint | Spring 2 [ 186 ] | Spring 2, Summer 1 [ 186, 195 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
Experiment name is 30-681594536. SRP486761
For SL4 and SL5. For this task, we need to confirm and sanity-check the Ravi 30-681594536 data that Rob 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. |
Experiment name is 30-681594536. SRP486761
Directory: /projects/tomato_genome/fnb/dataprocessing/SRP486761 For SL4 and SL5. For this task, we need to confirm and sanity-check the Ravi 30-681594536 data that Rob 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. |
Branch: https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3589
Re-run Directory SL4: /projects/tomato_genome/fnb/dataprocessing/SRP486761/nfcore-SL4/results/star_salmon
Re-run Directory SL5: /projects/tomato_genome/fnb/dataprocessing/SRP486761/nfcore-SL5/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"
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Robert Reid [ robertreid ] |
| Sprint | Spring 2, Summer 1 [ 186, 195 ] | Spring 2, Summer 1, Summer 2 [ 186, 195, 196 ] |
| Rank | Ranked higher |
Both SL4 and SL5 folders have the same 235 files.
SL4
55 bam files and bai files for each. Sizes look correct.
55 bedgraphs that are 120MB in size.
55 gzipped bed files that are 7 MB in size.
The tbi files seem to match the same 55 in number and all are small kb in size.
Sl5
55 bam files and bai files for each. Sizes look correct.
55 bedgraphs that are 120MB in size.
55 gzipped bed files that are 7 MB in size.
The tbi files seem to match the same 55 in number and all are small kb in size.
A few bedgraphs look smaller:
rw-rr- 1 mdavi258 tomato_genome 80M Jun 6 10:34 SRR27782293.scaled.bedgraph.gz
rw-rr- 1 mdavi258 tomato_genome 81M Jun 6 10:35 SRR27782329.scaled.bedgraph.gz
rw-rr- 1 mdavi258 tomato_genome 94M Jun 6 10:36 SRR27782312.scaled.bedgraph.gz
rw-rr- 1 mdavi258 tomato_genome 103M Jun 6 10:36 SRR27782326.scaled.bedgraph.gz
rw-rr- 1 mdavi258 tomato_genome 113M Jun 6 10:37 SRR27782325.scaled.bedgraph.gz
rw-rr- 1 mdavi258 tomato_genome 110M Jun 6 10:37 SRR27782311.scaled.bedgraph.gz
rw-rr- 1 mdavi258 tomato_genome 82M Jun 6 10:37 SRR27782294.scaled.bedgraph.gz
But that is most likely still within range of the others.
All looks good to proceed!
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Robert Reid [ robertreid ] | Molly Davis [ molly ] |
| 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. Thank you Robert Reid for making note of the unusual file sizes.
Need to compare multiqc reports pre- and post-SRA submission to sanity-check that the data deposition succeeded, using the resources created here.
Moving to DONE.
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
Used this document to run the pipeline: https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit