Question: Rtracklayer: Converting rlelist (Coverage) to bigwig
gravatar for datascientist28
3.3 years ago by
University of Washington
datascientist28410 wrote:

Hey all I'm trying to convert a rle-list to a bigwig file to view on a genome browser and am having trouble with my output BigWig. My Rle list has each chromosome as an item and them an rle vector of rpm coverage values at each basepair (screenshot shown here). I'm using from rtracklayer to convert to BigWig.

My problem is that when I'm exporting to bigWig, the track looks great but when viewing on IGV, certain chromosomes get left out completely (notably chromosome MT and X - which lead me to believe it has something to do with the names). (Seen here)

Interestingly, if I subset out just chromosomes MT and X (shown here), it exports just fine and the coverages for MT and X can be viewed in IGV.

Has anyone had this problem before??

coverage bigwig rtracklayer • 1.2k views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 3.3 years ago by datascientist28410
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