[IGBF-3545] Re-run nextflow Mark pollen tube data for SL4 and SL5 with data dowloaded from SRA - JIRA UNCC

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:
Support NSF pollen grant
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

relates to

IGBF-3498 Review SRA Submissions

Closed

IGBF-3499 Complete evaluation of RNA-Seq dataset submissions

Closed

Activity

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Molly Davis added a comment - 29/Jan/24 3:27 PM - edited

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

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Molly Davis added a comment - 29/Jan/24 3:27 PM - edited 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

7 older comments

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Molly Davis added a comment - 21/May/24 9:53 AM

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"

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Molly Davis added a comment - 21/May/24 9:53 AM 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"

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Robert Reid added a comment - 21/May/24 11:06 AM

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!

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Robert Reid added a comment - 21/May/24 11:06 AM 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!

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Molly Davis added a comment - 28/May/24 3:17 PM - edited

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

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Molly Davis added a comment - 28/May/24 3:17 PM - edited 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

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Ann Loraine added a comment - 04/Jun/24 9:56 AM

PR is merged into the "splicing analysis" repository.

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Ann Loraine added a comment - 04/Jun/24 9:56 AM PR is merged into the "splicing analysis" repository.

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Molly Davis added a comment - 05/Jun/24 3:16 PM

Review:

All quick load files are accounted for in both SL4 and SL5 directories
I made sure permission were accessible for group chmod -R g+w *
The merged files on bitbucket are correct

Moving to Done!

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Molly Davis added a comment - 05/Jun/24 3:16 PM Review : All quick load files are accounted for in both SL4 and SL5 directories I made sure permission were accessible for group chmod -R g+w * The merged files on bitbucket are correct Moving to Done!

People

Assignee:

Molly Davis

Reporter:

Molly Davis

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Watchers:

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Dates

Created:

17/Jan/24 3:05 PM

Updated:

05/Jun/24 3:16 PM

Resolved:

05/Jun/24 3:16 PM