STAR: Use multiple reference genomes at the same time

[Imchen]

Hi all,

I have meta-transcriptomic fastq files. I would like to use STAR aligner with multiple (~20) reference genomes at the same time (not one genome after another in the loop). Can someone please guide me through the appropriate steps? or point me to a tutorial?

Thanks,

[Alexander Dobin]

Hi Imchen,

You can generate the combined genome for all the 20 genomes, and map to it, provided that you have enough RAM.

If the genomes have a lot of similarity and you expect to see a lot of multimappers, you may need to scale up --winAnchorMultimapNmax (default=50) and --outFilterMultimapNmax (default=10)