My apologies if this has already been done and I lost track of the data somehow!

For this task, we need to align and deploy data from Azenta run 30-804059537 onto the SL4 / S_lycopersicum_Sep_2019 genome, using the S_lycopersicum_Sep_2019 assembly and accompanying gene annotations.

To-do:

• run the nextflow pipeline as per usual. Please use location /projects/tomato_genome/fnb/dataprocessing/30-804059537-KP/S_lycopersicum_Sep_2019 on the UNCC cluster
• create a branch in the code repo as usual
• commit to the branch the following files:

30-804059537_SL4_multiqc_report.html (renamed from multiqc_report.html)
30-804059537_SL4_salmon.merged.gene_counts.tsv (renamed from salmon.merged.gene_counts.tsv)

• create coverage graphs and junction files, as per usual
• move just the coverage graphs, bam files, and junction files to this location: /projects/tomato_genome/fnb/dataprocessing/30-804059537-KP/for_quickload/S_lycopersicum_Sep_2019/30-804059537 (We'll use this as the source directory for an rsync command that will copy these data over the data.bioviz.org host for visualization in IGB)