epiviz as genome viewer

[demis001]

Is it possible to load the bam file? I am trying to create publication quality figure for a manuscript. I have assembly data and want to show a specific locus with the assembled transcript and the reads in that locus. The image from IGV and UCSC genome browser isn't looks good. I just came across this tool and liked the presentation.

[jkanche]

Adding a pileup track for showing aligned reads is in our list of things to do. If you convert the bam file to a bigwig using deeptools or UCSC utilities, we can visualize the coverage as a line track in Epiviz. Let me know if thats something you would be interested in.

[demis001]

For the current work, showing pileup and splicing junction is necessary. I can convert the bam file to any format such as wig, bigwig or bedGraph. I installed as an app on my system BUT unable to see any menu that allows to load a custom track. Would you please tell me how to load custom track? I want to experiment with it to use in the future?

Thanks

[jkanche]

for loading custom data sets, checkout the epivizr package in bioconductor. This way you can load the data sets into R and visualize them with the epiviz app.