Directory: /nobackup/tomato_genome/Ravi_2022

Notes: Had to rerun because strandedness was reverse not unstranded after reviewing the multiqc report.

SL4 command & 2019 data:

./doIt.sh Ravi_samples_2022.csv /nobackup/tomato_genome/nfcore_rnaseq/S_lycopersicum_Sep_2019.fa /nobackup/tomato_genome/nfcore_rnaseq/S_lycopersicum_Sep_2019.gtf /nobackup/tomato_genome/nfcore_rnaseq/S_lycopersicum_Sep_2019.bed tomato.config 1> out.0.txt 2> err.0.txt

MultiQC Report Notes:

SL5 seemed to have no issues with strandedness after changing it to 'reverse'. I used the same sample.CSV file for the SL4 genome and ran nextflow and there seemed to be a strandedness warning on the mulitqc report. This happened for the 2021 data as well and I am unsure why these strandedness warning keep occurring. There are no issues with strandedness for the SL5 genome.

Next step: I will keep the multiqc report how it is and commit the files so they can be reviewed.

Double-check that the gene model annotations are correct. These are the gtf, bed, gff etc files used.

Checking SL4 annotation files:
Directory- /nobackup/tomato_genome/nfcore_rnaseq

I see no issues with the files themselves. Each contains annotations for the SL4 genome.

Next step: commit multiqc reports and sample.csv file.

Branch: https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3390

Note: Moved 2021 sample sheet to ExternalData folder as well as add the reports and csv file.

Ready for pull request. Please submit PR when ready.