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nanoporetech / megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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Different genomic coordinates between mappings.bam and mod_mappings.bam #320

Closed DidiCi closed 1 year ago

DidiCi commented 2 years ago

Good morning, I am using Megalodon for the detection of modified bases in human samples. I noticed that for some reads there is a difference in genomic coordinates (reference start, end and chromosome) between mappings.bam and mod_mappings.bam. Is this normal? If yes, why they change between the two files? Thank you in advance Diletta

marcus1487 commented 2 years ago

My best guess would be multi-mapping reads. The genomic coordinates should be the exact same for the same reads for these two outputs.