Hello Daniel, If I may suggest a 3rd-party program: the 'genomeCoverageBed' program ( part of BEDTools package, http://code.google.com/p/bedtools/ ) does exactly what you're looking for: reading a sorted BAM (or BED) file, and generates a textual BedGraph file (which can be converted directly to BigWig).
The program also allows extracting coverage of exons only, or just one strand. You can see usage examples here: http://groups.google.com/group/bedtools-discuss/web/community-usage-examples (examples 3,4,5) Or see more detailed examples about creating UCSC Genome browser tracks here: http://cancan.cshl.edu/labmembers/gordon/files/viz2.pdf (this is just a draft document). -gordon Daniel Klevebring wrote, On 09/03/2010 10:32 AM: > 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 ג‰ˆ50 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 > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
