Hi all,
In a Chip-SEQ pipeline, I import my mapped reads in to R, calculate coverage
with cov(), and run through a set of filters for peak selection, ending up
with a SimpleRleViewsList object. Now, I would like to visualize the file in
UCSC GB using the bigWig format, a task I normally accomplish by using the
rtracklayer's export on SimpleRleList objects, producing a bedGraph file
(that can then be converted to a bigWig).
The problem - when I use export() on a SimpleRleViewsList, the run-length
per-base information is lost, instead just producing ranges for each peak.
How can I convert a View on a Rle back to a per-base Rle?
Best regards,
Johannes Waage
Biotech Research and Innovation Center,
University of Copenhagen
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