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 10, Summer 1
Description
SRP252265
For SL4 and SL5.
For this task, we need to confirm and sanity-check the Mark 2020 pollen tube 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
Activity
PR is merged into the "splicing analysis" repository.
Should be fixed now! thank you for the catch!
Directory:/projects/tomato_genome/fnb/dataprocessing/SRP252265/nfcore-SL4/results/star_salmon
PR: https://bitbucket.org/hotpollen/splicing-analysis/pull-requests/17
24 bam files.
24 bai files.
HOWEVER!!
/projects/tomato_genome/fnb/dataprocessing/SRP252265/nfcore-SL4/results/star_salmon$ ll *bedgraph.gz.tbi | wc -l
23 index files for the bedgraphs!
And 23 bedgraph files!
The bam and bam index files are 24 and appear to be same size. So bedgraph stage is likley where issue lies.
Kicking it back to Molly!
Branch: https://bitbucket.org/mdavis4290/molly-2-splicing-analysis/branch/IGBF-3545
Re-run Directory SL4: /projects/tomato_genome/fnb/dataprocessing/SRP252265/nfcore-SL4/results/star_salmon
Re-run Directory SL5: /projects/tomato_genome/fnb/dataprocessing/SRP252265/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"
Re-run Directory SL4: /projects/tomato_genome/fnb/dataprocessing/SRP252265/nfcore-SL4
Re-run Directory SL5: /projects/tomato_genome/fnb/dataprocessing/SRP252265/nfcore-SL5
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/SRP252265/nfcore-SL4 module load sra-tools/2.11.0 vdb-config --interactive files=( SRR11284116 SRR11284117 SRR11284118 SRR11284119 SRR11284120 SRR11284121 SRR11284122 SRR11284123 SRR11284124 SRR11284125 SRR11284126 SRR11284127 SRR11284128 SRR11284129 SRR11284130 SRR11284131 SRR11284132 SRR11284133 SRR11284134 SRR11284135 SRR11284136 SRR11284137 SRR11284138 SRR11284139 ) for f in "${files[@]}"; do echo $f; prefetch $f; done
Execute:
chmod u+x prefetch.slurm
sbatch prefetch.slurm
Review:
Moving to Done!