choice of human genome before RNASeq mapping

Question

[Omics data mining]

Dear all,

I have RNASEQ data and want to map against the reference genome. I download human genome from ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/

Toplevel sequences unmasked: Homo_sapiens.GRCh38.dna.toplevel.fa.gz

Here, I found other format files such as

Toplevel soft/hard masked sequences: Homo_sapiens.GRCh38.dna_sm.toplevel.fa.gz Homo_sapiens.GRCh38.dna_rm.toplevel.fa.gz

Is it good choice if I go with repeat masked version Homo_sapiens.GRCh38.dna_rm.toplevel.fa.gz and star mapping RNASEQ on this repeat masked human genome?

[GenoMax]

Heng Li recently posted some thoughts about this very topic.

Answer 1

[grant.hovhannisyan]

Have a look here http://genomespot.blogspot.com.es/2015/06/mapping-ngs-data-which-genome-version.html