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Is there any plans to update phastCons scores package to support the GRCh38 assembly? I can only see the hg19 version in the release and development versions of Bioconductor.
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Hi Diego,
finally I did not produce the package with phastCons scores for GRCh38 until this latest release. You can find now in the lastest 3.1 release of BioC the PhastConsDb package phastCons7way.UCSC.hg38:
http://www.bioconductor.org/packages/release/data/annotation/html/phastCons7way.UCSC.hg38.html
these are phastCons scores for human GRCh38 derived from genome alignments to 6 other species. Please consult the original source of the data for further details at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons7way
cheers,
robert.
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Hi Robert, yes, I noticed and had already installed the package. Thank you for the announcement!
Forgot to tell that I have just pushed a bugfix affecting the method scores() to fetch phastCons values when the input GRanges had multiple-nucleotide ranges from un-ordered sequence names. You may have seen already this on the support site, but just in case. The versions with the bugfix are release 1.4.1 and devel 1.5.1 and will become available in the next 36 hrs or so.