This is a test version of Biostars. For the public version, visit https://www.biostars.org.
RNAseq, indexing with STAR

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
• 3,725 views • link
written by MOJ • MOJ

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?

• 0 views • link
written by h.mon h.mon

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

• 0 views • link
written by MOJ • MOJ

Can you maybe post the command you are using?

• 0 views • link
written by Matina Matina

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
• 0 views • link
updated by Ram Ram • written by MOJ • MOJ

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.

• 0 views • link
written by Matina Matina

Thanks Matina for the link. I worked for me..:)

• 0 views • link
written by shuksi1984 • shuksi1984

0 answers

No answers yet.

Log in to answer this question.

More posts like this