STAR options for DE genes in Arabidopsis Thaliana
0
0
Entering edit mode
5 months ago
arctic ▴ 40

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 \

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


# Star [alignment]

STAR \

--quantMode GeneCounts \

--genomeDir ./ATGenoIndices \

--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 \



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.).

STAR RNASeq HTSeq Arabidopsis thaliana • 189 views