Hi all
It is my first time working with STAR and I need to generate the genome index. However I have just the gff3 file intead of gtf. My gff3 file shows gene, mRNA, CDS, five_prime_UTR and three_prime_UTR annotation. Plus, everytime I try to run it, I am exceeding the RAM usage.
I am try this command:
STAR --runMode genomeGenerate \
--genomeDir ./genomeDir \
--genomeFastaFiles genomeDir/Gmax_275_v2.0.fa \
--runThreadN 8 \
--limitGenomeGenerateRAM 32000000000 \
--genomeChrBinNbits 10
--sjdbGTFfile genomeDir/Gmax_275_Wm82.a2.v1.gene.gff3 \
--sjdbGTFtagExonParentGene ID \
--sjdbGTFfeatureExon CDS \
--sjdbOverhang 99
Am I doing it right? It looks it is not working for me.
Thank you all
•
written
by
valopes •
1 answer
Despite the name, the sjdbGTFfile parameter accepts GFF3, we have tried this without problems. Well, RAM usage was high with the default settings, if I remember correctly. We needed about 300GB for generating the index for our 670Mb/33k scaffolds genome. Generating an index for the Salmon genome required almost 1TB. There are parameter settings that should allow for much lower RAM usage. See: http://seqanswers.com/forums/showthread.php?t=27470
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