Proper sequence length and genome for GRC

thelovelab / tximeta

Transcript quantification import with automatic metadata detection

https://thelovelab.github.io/tximeta/

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Proper sequence length and genome for GRC #3

Closed mikelove closed 4 years ago

mikelove commented 6 years ago

Need to make call to NCBI or Ensembl for GRC-based genomes, instead of current hack of converting to UCSC, then GenomeInfoDb::SeqInfo()

mikelove commented 6 years ago

Current solution is to use call to UCSC for "chr1" genomes (via GenomeInfoDB) and Ensembl for "1" genomes (via ensembldb). This needs a technical review from Bioconductor core team or other knowledgeable folks.