STAR aligment generating genome index

Question

[biology_inform]

Hi everyone, I am a newbie in RNA-Seq analysis. So I am going to use STAR and as you know there are some parameters when we are running it.

--runThreadN NumberOfThreads
--runMode genomeGenerate
--genomeDir /path/to/genomeDir
--genomeFastaFiles /path/to/genome/fasta1 /path/to/genome/fasta2 ...
--sjdbGTFfile /path/to/annotations.gtf
--sjdbOverhang ReadLength-1

Among those, what should be the number of threads for one fastq file and approximately how much time will it take (I am using a HPC) My organism is human btw Thanks in advance

[brunobsouzaa]

So, for generating genome index, you're not going to use any fastq file, this will be only for alignment step.

Regarding the number of threads, the best way is to check how many threads you have available. In my case, I like to use Nthreads - 4. But I have a local server available!

[biology_inform]

Thanks for your help. So in HPC is 28 okay?

Answer 1

[pmonsieurs]

I used the Human genome fasta file as available on http://ftp.ensembl.org/pub/current_fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz , and GTF file from http://ftp.ensembl.org/pub/current_gtf/homo_sapiens/Homo_sapiens.GRCh38.105.gtf.gz

It took around 25 minutes, also on a HPC using 28 threads. I have to admit that I did not do an optimalization on the number of threads to use (overhead might become the bottleneck when using 28 threads).

[biology_inform]

yes I run with the same parameters and mine was took approx 25-26 min. Again thx for the answer :)