Hi, I'm currently setting up a local mirror of a genome browser in order to visualize NGS data internally. The main type of data is human exome data, where we have now ≈50 exomes sequenced.
I have been following the progress of BAM support in UCSC GB and it looks very promising. One thing that I however miss is to be able to display density plots directly from BAM files, either as 1) a plot with coverage along the y-axis, or 2) as a density with a color indicating coverage. I attached a screendump where my suggestion 1) would be similar to the Enhancer H3K4 track and the suggestion 2) would be similar to the CRG Align tracks (ie scale from white to black if coverage is 0-50, otherwise black). It would also be awesome if it would be possible to pick custom colors in the settings for each track, instead of being locked to black and gray. If I understand correctly, samtools-c is able to create pileups, which could then be used to create a bedgraph on the fly. I really don't want to create a separate set of bedgraph files for each sample. Thanks a lot, Daniel Klevebring
-- Contact information: Daniel Klevebring, Ph. D. Department of Medical Epidemiology and Biostatistics Karolinska Institute Nobels Väg 12A, P. O. Box 281 SE-17 177 Solna Sweden Phone: +46 704 71 65 91 (Mobile)
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