I'm going through the nanopolish part of the tutorial on WSL. It has mostly been running smoothly, generating the proper files etc. But the file output is different from the preview results in the tutorial. For example, the files example_nanopolish-freq-perCG.tsv and freq-perCG-combStrand should get a coverage of 7 according to the tutorial, but mine is consistently generating a coverage of 1 or 2:
® example_nanopolish-freq-perCG.tsv
Chr Pos_start Pos_end Coverage Methylation Strand
NC_000913.3 3499494 3499495 1 1 -
NC_000913.3 3499526 3499527 1 1 -
NC_000913.3 3499546 3499547 1 1 -
NC_000913.3 3499562 3499563 1 1 +
NC_000913.3 3499563 3499564 1 1 -
NC_000913.3 3499591 3499592 1 1 -
NC_000913.3 3499597 3499598 1 1 -
NC_000913.3 3499630 3499631 1 1 +
NC_000913.3 3499631 3499632 1 1 -
® freq-perCG-combStrand
Chr Pos_start Pos_end Coverage Methylation
NC_000913.3 3499493 3499494 1 1
NC_000913.3 3499525 3499526 1 1
NC_000913.3 3499545 3499546 1 1
NC_000913.3 3499562 3499563 2 1
NC_000913.3 3499590 3499591 1 1
NC_000913.3 3499596 3499597 1 1
NC_000913.3 3499630 3499631 2 1
NC_000913.3 3499640 3499641 2 1
NC_000913.3 3499653 3499654 1 1