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estimate promoter activity from bam file #3

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jonathangoeke opened this issue Dec 5, 2019 · 2 comments
Open

estimate promoter activity from bam file #3

jonathangoeke opened this issue Dec 5, 2019 · 2 comments
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enhancement New feature or request

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@jonathangoeke
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Implement an option to estimate promoter activity from bam files (currently proActiv requires the junction files from TopHat2 or STAR)
@jonathangoeke jonathangoeke added the enhancement New feature or request label Dec 5, 2019
@jleechung
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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
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ninjaxfy commented Oct 8, 2021

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.

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@jonathangoeke @ninjaxfy @jleechung