4 days ago by
UK / London
Hi, it is most likely the UCSC Genome Browser where they have added multiple custom tracks and hidden most of the other default tracks. The easiest way to upload your data to the UCSC is in bedgraph format, with strand-specific read coverage of course.
HOMER has a nice UCSC export function that should work on any aligned BAM file, and it will output strand-specific information if you specify
For forward and reverse read tracks, you should just output forward and reverse reads separately from your aligned BAM into 2 files, and then work these into BED or bedgraph format. To output forward or reverse reads, I believe that you can use SAMtools: Samtools View: Only Forward Or Reverse Strand
Further information about UCSC custom tracks can be found here: http://genome.ucsc.edu/goldenPath/help/customTrack.html
It may take you some reading to see all of the possible ways to display the data, but it is quite a powerful tool. Once you upload your data, you can then even share the URL to collaborators and they can then view the same data until the session expires.