Hello,
I noticed that Bismark paired-end runs give you an output with start/stop genomic positions only for the first read, but not for its mate.
As the two mates overlap but do not have identical start/stop positions, is there a recommended way to discern the start/stop position of the second read, without having to re-align it to the genome or to its mate?
I'm aware that methylation_extractor takes care of this, but I'd be interested in the full sequence of paired-end runs in addition to the methylation call.
Any suggestions would be greatly appreciated!
I noticed that Bismark paired-end runs give you an output with start/stop genomic positions only for the first read, but not for its mate.
As the two mates overlap but do not have identical start/stop positions, is there a recommended way to discern the start/stop position of the second read, without having to re-align it to the genome or to its mate?
I'm aware that methylation_extractor takes care of this, but I'd be interested in the full sequence of paired-end runs in addition to the methylation call.
Any suggestions would be greatly appreciated!
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