[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


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 

any hint on how to achieve this goal will be very much appreciated,


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