[BioC] working with genome-wide phastCons scores
Robert Castelo
robert.castelo at upf.edu
Wed Oct 23 18:03:46 CEST 2013
dear list,
i have to pretty intensively work with genome-wide phastcons scores and
instead of repeatedly interrogate them through the internet via the UCSC
genome browser with 'rtracklayer', i'd prefer to do a bulk download of
the *.phastCons46way.wigFix.gz files (about 0.6Gb) at
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/vertebrate
and then import them into R storing the information in some memory
efficient data structure (Rle?) that provides me also an efficient way
to query the phastcons score at any position of the human genome.
all documentation and messages i've been able to retrieve through google
and the BioC list correspond to use cases that involve a small fraction
of the genome which can be handled by 'rtracklayer' with an internet
connection.
any hint on how to achieve this goal will be very much appreciated,
thanks!
robert.
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