the -p option about a overlapping read

dpryan79 / MethylDackel

A (mostly) universal methylation extractor for BS-seq experiments.

MIT License

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the -p option about a overlapping read #114

Closed gill0110 closed 3 years ago

gill0110 commented 3 years ago

I want to know how to set the -p option to handle overlopping reads ? I use MethylDackel extract for the inputfile required by methylKit, and use the commend:

nohup MethylDackel extract -o fa1.1 --CHG --CHH --methylKit Fana.fasta fa1.1.sort.bam >>MethylDackel.log 2>&1 &

dpryan79 commented 3 years ago

Any value for p > 0 should properly handle overlapping portions of reads (the phred score for the overlapping portion of one of the reads is converted to 0 internally).