Run nextflow for the dataset in:

/projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

Kindly run the nf-core pipeline in this location:

• /nobackup/tomato_genome/mark-2022-timeseries

Note on attached files:

• multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html
• Link: https://drive.google.com/drive/u/1/folders/1GJnZefP-7TE-ch-c0lblGZMOqpwSgZRK
• 2023-01-18_timeseries_multiqc_report.html - MultiQC report from re-running nextflow (Molly's new work)\
• sample.csv - new samples file used to re-run nextflow (Molly's new work)