Re-run Directory: /projects/tomato_genome/fnb/dataprocessing/SRP499796/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/SRP499796/nfcore-SL4
module load sra-tools/2.11.0
vdb-config --interactive

files=(
SRR28558218
SRR28558219
SRR28558220
SRR28558221
SRR28558222
SRR28558223
SRR28558224
SRR28558225
SRR28558226
SRR28558227
SRR28558228
SRR28558229
SRR28558230
SRR28558231
SRR28558232
SRR28558233
SRR28558234
SRR28558235
SRR28558236
SRR28558237
SRR28558238
SRR28558239
SRR28558240
SRR28558241
)

for f in "${files[@]}"; do echo $f; prefetch $f;  done

Execute:

chmod u+x prefetch.slurm

sbatch prefetch.slurm

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=1-24

#setting up where to grab files from
file=$(sed -n -e "${SLURM_ARRAY_TASK_ID}p"  /projects/tomato_genome/fnb/dataprocessing/SRP499796/nfcore-SL4/Sra_ids.txt)


cd /projects/tomato_genome/fnb/dataprocessing/SRP499796/nfcore-SL4
module load sra-tools/2.11.0

echo "Starting faster-qdump on $file";

cd /projects/tomato_genome/fnb/dataprocessing/SRP499796/nfcore-SL4/$file

fasterq-dump ${file}.sra

perl /projects/tomato_genome/scripts/validateHiseqPairs.pl ${file}_1.fastq ${file}_2.fastq

cp ${file}_1.fastq /projects/tomato_genome/fnb/dataprocessing/SRP499796/nfcore-SL4/${file}_1.fastq
cp ${file}_2.fastq /projects/tomato_genome/fnb/dataprocessing/SRP499796/nfcore-SL4/${file}_2.fastq 

echo "finished"

Execute:

chmod u+x fasterdump.slurm

sbatch fasterdump.slurm

Nextflow Pipeline ran successfully with SL4 and SL5 genome
Directory:

• /projects/tomato_genome/fnb/dataprocessing/SRP499796/nfcore-SL4
• /projects/tomato_genome/fnb/dataprocessing/SRP499796/nfcore-SL5

MultiQC report notes: No errors or warnings were present in the report. The output files are named 'SRP499796_SL4_multiqc_report.html' & 'SRP499796_SL5_multiqc_report.html'.

Next steps:
Commit multiqc reports and csv sample file to Flavonoid repo on bitbucket
Change sorted bam names
Create junction files
Create Coverage graphs

Branch: https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3688

• ARE-120min-analysis/SRP499796.csv
• ARE-120min-analysis/SRP499796_SL4_multiqc_report.html
• ARE-120min-analysis/SRP499796_SL5_multiqc_report.html

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

Directories:
/projects/tomato_genome/fnb/dataprocessing/SRP499796/nfcore-SL4/results/star_salmon
/projects/tomato_genome/fnb/dataprocessing/SRP499796/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"

The SL4 Folder
The TSV files look complete.
All the bedgraphs are about 45MB in size and there are 24 files.
All the bed files are about 4.5MB in size and there are 24 files.
All tbi files are ~ 70kb and there are 24 bedgraph versions and 24 bed versions.
Bams are 2.8 GB in size and there are 24.

The SL5 Folder
The TSV files look complete. 36K number of lines looks correct. for SL5.
All the bedgraphs are about 45MB in size and there are 24 files.
All the bed files are about 4.5MB in size and there are 24 files.
All tbi files are ~ 70kb and there are 24 bedgraph versions and 24 bed versions.
Bams are 2.8 GB in size and there are 24.

This looks correct! Passing it back to Molly.

Branch: https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3688
PR: https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/44

• ARE-120min-analysis/SRP499796.csv
• ARE-120min-analysis/SRP499796_SL4_multiqc_report.html
• ARE-120min-analysis/SRP499796_SL5_multiqc_report.html

PR is merged. Moving to "ready for testing."

To test, review the files. If no problems observed, move forward to "Done."

I reviewed the files as follows:

• Checked that I could open the MultiQC files in my Web browser. I was able to open and review both.
• Checked that the data are reported as "unstranded" in the run configuration file SRP499796.csv. They were.
• Checked that RSeQC reported an about equal number of sense and antisense reads (with respect to gene models provided to the pipeline). It did.
• However, I notice there is no sample sheet available in the repository for this data set. We will need to provide this to set up the data in IGB quickload. I made a ticket for it with more details.

Testing passes. Moving to DONE.