This data set from Arabidopsis thaliana contains six samples of FACS-sorted sperm and vegetative cells from mature pollen. The publication is here: https://pubmed.ncbi.nlm.nih.gov/36515615/

This would be a useful reference data set for our studies, as the authors reported many differentially and alternatively spliced genes between sperm and vegetative cells harvested from mature Arabidopsis pollen.

For this task

• download the data as fastq files from SRA
• align fastq files using nf-core/rnaseq vs. TAIR10 genome (see link below)
• for alignment parameters, use original publication (referenced above) and their parameters that they used in their experiment. Every RNA-Seq to genome alignment tool requires the user to define a maximum intron size parameter. Never use the default! Customize for your species!
• align using same maxIntron parameter reported in the methods section for the paper
• for the above, make a new "config" file
• create coverage graphs
• create junction files

Use this reference genome for alignment:

• http://lorainelab-quickload.scidas.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit

Create the "fasta" file from the above 2bit file using blat suite tools on cluster. The program you need is 2bitToFa (I think to load it, you have to use "module load blatsuite" or something like that. Use "module avail" to find the correct module name.)

2bitToFa command:

twoBitToFa A_thaliana_Jun_2009.2bit A_thaliana_Jun_2009.fa