choice of human genome before RNASeq mapping

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?

human genome ensembl rnaseq mapping

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updated 8.4 years ago by grant.hovhannisyan

• written 8.4 years ago by Omics data mining

Heng Li recently posted some thoughts about this very topic.

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written 8.4 years ago by GenoMax

1 answer

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

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written 8.4 years ago by grant.hovhannisyan

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