estimate promoter activity from bam file

GoekeLab / proActiv

Estimation of Promoter Activity from RNA-Seq data

https://goekelab.github.io/proActiv/

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estimate promoter activity from bam file #3

Open jonathangoeke opened 4 years ago

jonathangoeke commented 4 years ago

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

jleechung commented 4 years ago

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 commented 2 years ago

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.