BSgenome.Hsapiens.UCSC.hg38 vs BSgenome.Hsapiens.NCBI.GRCh38
1 answer
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.
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Maybe the naming convention for the chromosomes?
UCSC usually prefix the chromosome with
chr, NCBI doesn't.From the examples in the manuals:
BSgenome.Hsapiens.NCBI.GRCh38.pdf
genome[["1"]]BSgenome.Hsapiens.UCSC.hg38.pdf
genome$chr1 # same as genome[["chr1"]]fin swimmer
It is the same question as "the difference between UCSC and NCBI genomes". Why don't you load them and compare?