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.
Question: BSgenome.Hsapiens.UCSC.hg38 vs BSgenome.Hsapiens.NCBI.GRCh38
6 weeks ago by
ZheFrench • 140
ZheFrench • 140 wrote:
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25 days ago by
igor ♦ 6.9k
igor ♦ 6.9k 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
- 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.
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