Deleted:STAR options for DE genes in Arabidopsis Thaliana

Question

[arctic]

Hi all, I am relatively new to the field. I would be very grateful to have a second opinion on below options from someone with STAR experience (particularly in the context of AT or plant species).

Star [create genomic indices]

STAR \ 
--runMode genomeGenerate \

--genomeDir ...\

--genomeFastaFiles ./Arabidopsis_thaliana.TAIR10.dna.toplevel.fa \

--sjdbGTFfile ./Arabidopsis_thaliana.TAIR10.50.gtf \

--sjdbOverhang 74 \    
\## My ReadLength-1

--genomeSAindexNbases 12     
\## log2(GenomeLength)/2 - 1=12.41

Star [alignment]

STAR \

--quantMode GeneCounts \

--genomeDir ./ATGenoIndices \

--readFilesIn .... \

--outFileNamePrefix ... \

--outFilterMultimapNmax 20 \

--alignSJoverhangMin 8 \

--alignSJDBoverhangMin 8 \

--outFilterMismatchNmax 8 \

--alignIntronMin 35 \

--alignIntronMax 2000 \    
\## 99.3% of introns in AT are below this size based on doi:10.3390/genes8080200 

--alignMatesGapMax 100000 \

--readFilesCommand zcat

I have been trying to find the optimum settings using available literature, however the variety has been overwhelming. I eventually ended up pasting together above options from few references that appeared to be more in line with the analysis I am hoping to perform ( Which is simple DE analysis at gene level.).

Many thanks for your time and help in advance,