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 \    
\## 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,

STAR RNASeq HTSeq Arabidopsis thaliana • 189 views
ADD COMMENT

Login before adding your answer.

Traffic: 1586 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6