junctionCount : can we add a flag to convert strands info

LieberInstitute / jaffelab

R package with commonly used functions by the Jaffe lab

http://lieberinstitute.github.io/jaffelab

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junctionCount : can we add a flag to convert strands info #4

Open andrewejaffe opened 4 years ago

andrewejaffe commented 4 years ago

Specifically, when strand information is coded as "?". Right now, these junctions are dropped. It would be good to instead offer the option of converting the "?" to the un-stranded character "*", since some BAM files seem to encode this as unstranded

lcolladotor commented 3 years ago

I think that @Nick-Eagles and @gpertea worked on some related issues on SPEAQeasy.