Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:2
-
Epic Link:
-
Sprint:Fall 1 - Sep 5, Summer 8 2023 Aug 21
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
Activity
Faster Dump Script:
#! /bin/bash #SBATCH --job-name=fastqdump_SRR #SBATCH --partition=Orion #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --mem=40gb #SBATCH --output=%x_%j.out #SBATCH --time=24:00:00 #SBATCH --array=1-48 #setting up where to grab files from file=$(sed -n -e "${SLURM_ARRAY_TASK_ID}p" /projects/tomato_genome/fnb/dataprocessing/SRP438952/Sra_ids.txt) cd /projects/tomato_genome/fnb/dataprocessing/SRP438952 module load sra-tools/2.11.0 echo "Starting faster-qdump on $file"; cd /projects/tomato_genome/fnb/dataprocessing/SRP438952/$file fasterq-dump ${file}.sra perl /projects/tomato_genome/scripts/validateHiseqPairs.pl ${file}_1.fastq ${file}_2.fastq cp ${file}_1.fastq /projects/tomato_genome/fnb/dataprocessing/SRP438952/${file}_1.fastq cp ${file}_2.fastq /projects/tomato_genome/fnb/dataprocessing/SRP438952/${file}_2.fastq echo "finished"
Execute:
chmod u+x fasterdump.slurm
sbatch fasterdump.slurm
Nextflow Pipeline ran successfully with SL5 genome
Directory: /projects/tomato_genome/fnb/dataprocessing/SRP438952
MultiQC report notes: No errors or warnings were present in the report. The output file is named 'SRP438952_multiqc_report.html'.
Cluster Note: I had to email OneIT UNCC due to issues with logging in on the cluster. Their response:
We narrowed this issue down to one of our interactive nodes, str-i2, which was unusually overloaded. We rebooted it, and things seem to be back to normal. Please try your login again, and let me know if the issue persists.
Next steps:
- Commit CSV and multiqc report to Splicing repo on bitbucket
- Change sorted bam names
- Create junction files
- Create Coverage graphs
Launch renameBams.sh script:
./renameBams.sh
Launch Scaled Coverage graphs script:
./sbatch-doIt.sh .bam bamCoverage.sh >jobs.out 2>jobs.err
Launch Junction files script:
./sbatch-doIt.sh .bam find_junctions.sh >jobs.out 2>jobs.err
Directory: /projects/tomato_genome/fnb/dataprocessing/SRP438952/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"
Reviewer: [~RobertReid]
Checking things.
- All of the file types have 48 total files as expected
- There is a tbi file for every gz file.
- The sizes of all the files are similar to one another the tbi index files.
- The FJ.bed.gz files are similar in size at around 4MB +- 4.
- The scaled bedgraphs are all 30MB to 130MB in size. Similar enough!
- There is a total of 96 tbi files as expected (48 scaled and 48 FJ)
- There is a total of 96 gz files as expected (48 scaled and 48 FJ)
All looks as expected!
Great job.
Branch: https://bitbucket.org/mdavis4290/molly-splicing-analysis/branch/IGBF-3424
Includes:
- MultiQC Report
- CSV
[~aloraine]
Re-run Directory:/projects/tomato_genome/fnb/dataprocessing/SRP438952/nfcore-SL5
Prefetch SRR Script:
Execute: