Directory of original files that are NOT renamed: /projects/tomato_genome/rnaseq/muday144-timeSeries-checkReadMEFIRST/00_fastq

SL4 Nf-core run location: /projects/tomato_genome/fnb/dataprocessing/muday-144/nfcore-SL4

Nextflow Pipeline ran successfully with SL4 genome
Directory: /projects/tomato_genome/fnb/dataprocessing/muday-144/nfcore-SL4
MultiQC report notes: No errors or warnings were present in the report. The output file is named 'muday-144-SL4_multiqc_report.html'.

Next Steps: Commit Multiqc report to documentation in flavonoid repo. Create Coverage graphs and junction files.

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

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]

Note: There were two warnings but no errors that I saw.

Branch: https://bitbucket.org/mdavis4290/molly3-flavonoid-rnaseq/branch/IGBF-3450

Note: Includes the SL4 Mutliqc report.

[~aloraine]

Change requests:

1) "chmod" the entire contents of nfcore-SL4 to make them group editable

This is so that I can move the bam, bedgraph, and junction files over to another directory for copying to the data host. I don't want to make copies due to the risk of error and also to save disk space and energy.

2) Add this file to your branch:

• /projects/tomato_genome/fnb/dataprocessing/muday-144/nfcoreSL4/results/star_salmon/salmon.merged.gene_counts.tsv

as file:

• 72_F3H_PollenTube/muday-144-SL4_salmon.merged.gene_counts.tsv

Please add it to your branch and then submit a PR.

Thank you!

Ann

Double-checking:

The renamed fastq files were NOT used here. Is this right? That is, the original files with their original names were processed, the same exact files that we got from the sequencer?

These are the original files that are NOT renamed. Straight from the sequencer!
This can be confirmed in the README in the original directory: /projects/tomato_genome/rnaseq/muday144-timeSeries-checkReadMEFIRST/00_fastq

Results should also now be editable.
[~aloraine]

Pull Request: https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/24

Testing suggestions:

• Compare multiqc reports from SL4, SL5 assemblies. PCA plots should mostly match.

[~molly]: please try again with the "chmod-ing"

I need to move these files into position for transferring to data.bioviz.org, like so:

[aloraine@str-i1 muday-2022-timeseries]$ pwd
/projects/tomato_genome/fnb/dataprocessing/muday-144/for_quickload/S_lycopersicum_Sep_2019/muday-2022-timeseries
[aloraine@str-i1 muday-2022-timeseries]$ mv ../../../nfcore-SL4/results/star_salmon/*.bam .
mv: cannot move '../../../nfcore-SL4/results/star_salmon/7-are-15-min-28C.bam' to './7-are-15-min-28C.bam': Permission denied

I need to move all the bam, bam index, coverage graph, coverage graph index, junction, junction index files over to /projects/tomato_genome/fnb/dataprocessing/muday-144/for_quickload/S_lycopersicum_Sep_2019/muday-2022-timeseries but can't because of how the permissions are set.

I would like to take some pictures of genes before tomorrow if at all possible! But I don't want to waste a lot of disk space and energy to meet a deadline

chmod g+w /projects/tomato_genome/fnb/dataprocessing/muday-144/nfcore-SL4/results
chmod -R g+w *

Moved or copied nf-core output files to HPC file system location: /projects/tomato_genome/fnb/dataprocessing/muday-144/for_quickload/S_lycopersicum_Sep_2019/muday-2022-timeseries

On data.bioviz.org host, launched "screen" session and commenced copying nf-core output files to data.bioviz.org with:

cd /mnt/igbdata/hotpollen/S_lycopersicum_Sep_2019
rsync -rz aloraine@10.16.115.244:/projects/tomato_genome/fnb/dataprocessing/muday-144/for_quickload/S_lycopersicum_Sep_2019/muday-2022-timeseries .

Added new SL4 data to the annots.xml configuration files for visualization in IGB. Updated "main" branch of https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/

Review passes:

• counts file is added to the repo
• data files are added to data.bioviz.org for visualization and permissions set to allow delivery via the Web server
• also added multiqc report and its input data to the data.bioviz.org deployment site for easier visualization

Note that these data are NOT using renamed labels. The files that were processed match the original file names from the sequencer.

Moving to ready for testing.

Testing:

• Count file is present in repo: 72_F3H_PollenTube/muday-144-SL4_salmon.merged.gene_counts.tsv
• SL5 (PT time GM lab) and SL4 (PT time GM lab) datasets for Muday-144 are present and accessible in IGB quickload
• Found report and input data on deployment site here: https://data.bioviz.org/hotpollen/S_lycopersicum_Sep_2019/muday-2022-timeseries/

Moving to done!