index build #11
Description
Hi,
I have reviewed the documentation and parameter descriptions of the proseq2.0 processing pipeline, and I have several questions. For experiments that include spike-in controls, should I process the two species separately using two independent BWA indices, or should I combine the FASTA files from both species and build a single merged index? In addition, since I am using reference genome FASTA files downloaded from GENCODE, do I need to manually add the rRNA (rDNA) sequences to the reference genome?