I have been looking for the latest Macaque genome (mmul10) sequence definition for the BSgenome package; but can't find it. Is it available? If not, is it in progress and when would it be available?
Right. Although it's not exactly the same. The BSgenome wrapper adds a few conveniences like the ability to rename the seqlevels, "inject" SNPS, properly handle circular sequences, and a cleaner sequence order. Also not all workflows support TwoBitFile objects (even though they probably should).
Note that it's relatively easy to forge your own BSgenome package. The process is documented in the "How to forge a BSgenome data package" vignette (linked on the BSgenome landing page).
Macaque is one of those organisms for which we have traditionally tried to keep up by providing new BSgenome data packages as new assemblies become available. We'll add one for the latest assembly, Mmul_10 (will be BSgenome.Mmulatta.UCSC.rheMac10, following the usual naming scheme).
Ah, thanks, Herve. I forgot to ask about creating my own BSgenome package. Thanks for the link. Will look into that. Do you have a time estimate of when the BSgenome.Mmulatta.UCSC.rheMac10 will be ready?
Right. Although it's not exactly the same. The BSgenome wrapper adds a few conveniences like the ability to rename the seqlevels, "inject" SNPS, properly handle circular sequences, and a cleaner sequence order. Also not all workflows support TwoBitFile objects (even though they probably should).
Note that it's relatively easy to forge your own BSgenome package. The process is documented in the "How to forge a BSgenome data package" vignette (linked on the BSgenome landing page).
Macaque is one of those organisms for which we have traditionally tried to keep up by providing new BSgenome data packages as new assemblies become available. We'll add one for the latest assembly, Mmul_10 (will be BSgenome.Mmulatta.UCSC.rheMac10, following the usual naming scheme).
H.
Ah, thanks, Herve. I forgot to ask about creating my own BSgenome package. Thanks for the link. Will look into that. Do you have a time estimate of when the BSgenome.Mmulatta.UCSC.rheMac10 will be ready?
I forgot to mention that the functionality is in the rtracklayer package.
Thanks, James. I will see if I can work with that.