Question: BSgenome.Hsapiens.UCSC.hg38 vs BSgenome.Hsapiens.NCBI.GRCh38
0
gravatar for ZheFrench
6 months ago by
ZheFrench210
France
ZheFrench210 wrote:

I am wondering what is the difference between this two reference package in R ? hg38 and GRCh38 should be same sequence assembly, right ? So what the point of creating this two reference package to access raw sequence.

assembly version R genome • 381 views
ADD COMMENTlink modified 6 months ago by igor7.6k • written 6 months ago by ZheFrench210
1

Maybe the naming convention for the chromosomes?

UCSC usually prefix the chromosome with chr, NCBI doesn't.

From the examples in the manuals:

fin swimmer

ADD REPLYlink modified 6 months ago by zx87547.1k • written 6 months ago by finswimmer11k
1

It is the same question as "the difference between UCSC and NCBI genomes". Why don't you load them and compare?

ADD REPLYlink written 6 months ago by zx87547.1k
1
gravatar for igor
6 months ago by
igor7.6k
United States
igor7.6k wrote:

There are actually many different versions of hg38/GRCh38. This post by lh3 describes the human reference genome landscape very nicely: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Specific discrepancies:

  • Inclusion of ALT contigs.
  • Padding ALT contigs with long “N”s.
  • Inclusion of multi-placed sequences.
  • Not using the rCRS mitochondrial sequence.
  • Converting semi-ambiguous IUB codes to “N”.
  • Using accession numbers instead of chromosome names.
  • Not including unplaced and unlocalized contigs.
ADD COMMENTlink modified 6 months ago • written 6 months ago by igor7.6k
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