RNAseq, indexing with STAR

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6.7 years ago

MOJ • 0

I am wrking on RNAseq. I am using STAR for indexing. It generates all the files except the genome file.I am running the command on 30G RAM and 400G hard disk and 2 runthread. It took 2 days and is still running. Any opinion will be appreciated

RNA-Seq rna-seq • 3.0k views

ADD COMMENT • link 6.7 years ago by MOJ • 0

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What is the assembly quality / level? Hundreds of thousands contigs, hundreds or a few thousands scaffolds, or tens of chromosomes? What is the size in gigabytes of the genome file?

ADD REPLY • link 6.7 years ago by h.mon 35k

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human.refseq.gff.gtf is 227M Genomic.fna is 3.1GB

ADD REPLY • link 6.7 years ago by MOJ • 0

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Can you maybe post the command you are using?

ADD REPLY • link 6.7 years ago by Matina ▴ 250

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When I used following command, several SA index files are generated.

/path/to/star/STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /path/to/star/genome_file --genomeFastaFiles /path/to/star/GCF_000001405.31_GRCh38.p5_genomic.fna --sjdbGTFfile /path/to/star/human.refseq.gff.gtf --sjdbOverhang 100 --limitGenomeGenerateRAM=8825541333

ADD REPLY • link updated 6.7 years ago by Ram 44k • written 6.7 years ago by MOJ • 0

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I cant see anything wrong with this command. This is weird indeed. Why don't you try and post your question here at the official rna-star forum. The developer of STAR (Alex Dobin) is great - always replies to posts and he is super helpful.