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 1, Spring 2, Spring 3, Spring 4
Description
SRP438952
For this task, we need to confirm and sanity-check the seedling and mature pollen 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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Activity
The original mature pollen and seedlings data on the cluster was not run with SL4, only SL5. So the next step would be to run the original data with SL4 and then compare the rerun SL4 report with the original report.
Molly Davis - please see above comment on how to test. I don't know if you have already compared the files or not?
If not, it would be good to do that now.
The QC reports provide a great overview of a data processing run. Comparing the QC reports pre- and post-SRA submission will tell us a lot. For example, if there are a big differences between the pre- and post-SRA submission files, the QC report will likely show it.
Suggestions for testing:
- Check that these new quality control reports are consistent with the original quality control reports obtained when we processed the original, pre-submission data files. The results should be the same.
Re-run Directory:/projects/tomato_genome/fnb/dataprocessing/SRP438952/nfcore-SL4
Prefetch SRR Script:
#! /bin/bash #SBATCH --job-name=prefetch_SRR #SBATCH --partition=Orion #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --mem=4gb #SBATCH --output=%x_%j.out #SBATCH --time=24:00:00 cd /projects/tomato_genome/fnb/dataprocessing/SRP438952/nfcore-SL4 module load sra-tools/2.11.0 vdb-config --interactive files=( SRR24685698 SRR24685699 SRR24685700 SRR24685701 SRR24685702 SRR24685703 SRR24685704 SRR24685705 SRR24685706 SRR24685707 SRR24685708 SRR24685709 SRR24685710 SRR24685711 SRR24685712 SRR24685713 SRR24685714 SRR24685715 SRR24685716 SRR24685717 SRR24685718 SRR24685719 SRR24685720 SRR24685721 SRR24685722 SRR24685723 SRR24685724 SRR24685725 SRR24685726 SRR24685727 SRR24685728 SRR24685729 SRR24685730 SRR24685731 SRR24685732 SRR24685733 SRR24685734 SRR24685735 SRR24685736 SRR24685737 SRR24685738 SRR24685739 SRR24685740 SRR24685741 SRR24685742 SRR24685743 SRR24685744 SRR24685745 ) for f in "${files[@]}"; do echo $f; prefetch $f; done
Execute:
chmod u+x prefetch.slurm
sbatch prefetch.slurm
When I make the comparison ticket for mature pollen and seedling I will compare the mutliqc reports then so for now I will move this ticket to Done!