Hi all,

I have a small but important challenge set before me, that I've been unable
to solve. I need to aggregate all phastCon scores for 75-100 nt around all *
mus* exon splicesites. I've tried different approaches, such as downloading
the entire mulitz30way phastCon dataset from UCSC (too big to work with
smoothly), download using intersect with UCSC table browser and Galaxy
(limits me to 10 million data points, unfortunately), and fetching data
trough rtracklayer (too slow). Can anyone point me towards an elegant and
fast way to fetch datapoints for many genomic intervals? With around 22k
genes, with an average exon count of 8 times 100 nt, it seems I need to be
able to fetch around 20m data points.

I need to use the data as background in comparison to select upregulated
exons in a RNA-seq splice study.

All the best,

JW,

University of Copenhagen

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