estimate promoter activity from bam file

[jonathangoeke]

Implement an option to estimate promoter activity from bam files (currently proActiv requires the junction files from TopHat2 or STAR)

[jleechung]

BAM file usage implemented using GenomicAlignments package with readGAlignments and summarizeJunctions functions. Future work to be done includes reading/extracting only the reads that are needed to infer junction usage instead of the whole BAM file.

[ninjaxfy]

Hi: I'm trying to estimate promoter activity from bam files, and my question is that I use the given bam file in the proactiv package, but I did not get the result like the workflow.