I havent tried this, but have you attempted to run indelpe on single-end mapping results from novoalign converted to .map format?
Novoalign's mapping quality's are not recalculated for paired-end and you should see this from the `map mapstat` output.
I think Colin will be able to shed more light on this.
Novoalign's mapping quality's are not recalculated for paired-end and you should see this from the `map mapstat` output.
I think Colin will be able to shed more light on this.
Originally posted by myrna
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