Options for 'GeneCounts' in Arabidopsis Thaliana

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Dear all,

I am relatively new to the field and I am trying to use STAR to do alignment and count in Arabidopsis Thaliana. The variety of options found in the literature has been overwhelming.

A list of options I am considering to use is below. I wonder if these options seem reasonable? In particular, would there be a reason to change below three options for Arabidopsis from their default?

 - alignSJDBoverhangMin

 - outFilterMismatchNmax 

 - alignMatesGapMax 

Many thanks for your help and reply beforehand,

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 \

# Default 

--alignSJoverhangMin 8 \

# Default 

--alignSJDBoverhangMin 3 \

# Default  (alternative 8?)

--outFilterMismatchNmax 10 \

# Default (alternative 8?)

--alignIntronMin 35 \

--alignIntronMax 2000 \    

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

--alignMatesGapMax 0 \

# Default (alternative 100,000?) 

--readFilesCommand zcat