Problems to index reference genome and to align RNAseq

Question

[silas008]

I'm trying to align RNAseq data with STAR aligner. The reference genome for mice is split in 1-22 + X,Y and MT.

Should I create the reference genome index with splited chromosome or should I use a merged fasta file containing all of the individual chromosomes?

If I have indexed splited chromosomes, when I align the reads, should I do that on separated chromosomes or on merged fasta file?

Answer 1

[Brian Bushnell]

Index and map using a single fasta file containing all reference sequences.