Rsamtools pileup help
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JoeMG • 0
@joemg-15694
Last seen 19 months ago
Israel

Dear Rsamtools,

I'm hoping to use the pileup function to output a table like the below. My goal is to be strand sensitive, distiguish +/- (for paired-end), include indels, as well count of 5'starts and 3'stops. I have so far been unsuccessful coming up with an implementation of PileupParam to retrieve this information. Are you able to help? Thanks!

chr loc ref strand  A   T   C   G   a   t   c   g   Insertion   Deletion    Stops   Starts
1   888659  T   +   0   9   0   2   0   0   0   0   2:AG|1:AGAG 1:ATT   3   2
Rsamtools pileup • 609 views
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