STAR for alignment

[sbdk82]

I am trying to use STAR instead of Tophat, but I am bit confused. I already have the reference file and GTF file. So should I skip the "generate genome" and "generate genome with annotation" steps (4 and 5 in manual)?

If I directly use the following, should I keep my reference file under "/path/to/GenomeDir" ?

STAR --genomeDir /path/to/GenomeDir --readFilesIn /path/
to/read1 [/path/to/read2] --runThreadN <n> --<inputParameterName> <input 
parameter value(s)>

I have paired end reads, reference file and GTF file. Please help me which command I need to use.

[dpryan]

The "generate genome" and "generate genome with annotation" create an index that STAR uses for mapping. You can't skip those steps.

"/path/to/GenomeDir" is just an example name, you can keep things where ever you want and then just change that to match.

[sbdk82]

Thanks Devon !!

So I should use the following to build the index

STAR --runMode genomeGenerate --genomeDir <output directory> --genomeFastaFiles /path/reference.fa --runThreadN 5 --sjdbGTFfile <GTF file name>.