Hi,
Can the BSgenome.Hsapiens.UCSC.hg19 genome sequence package in Bioconductor be used instead of the provided sequence? The package is created using the files here http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
Is the sequence data for the hg19/GRCh37 release version of the human genome provided in the data files equivalent to BSgenome.Hsapiens.UCSC.hg19? I realize that Version 19 of the annotation is different from earlier releases, but are the sequences different?
Thanks,
Rick
Created by Rick Farouni rfarouni They probably should be identical. We are using hg19 as well but not the UCSC sequences explicitly. We use the ENCODE version of hg19 which has some small differences e.g. chrM sequence may be more recent and the chrY sequence has the PAR regions masked. But we dont include chrM and chrY in this challenge so it should probably not be any different. You will need to check this. If they are identical then you can certainly use the BSgenome sequence.
-Anshul.