estimate promoter activity from bam file

Question

estimate promoter activity from bam file

Opened this issue 5 years ago · 2 comments

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

Answer 1 · 2020-06-22T10:12:06.000Z

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.

Answer 2 · 2021-10-08T07:06:28.000Z

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.