rhallPB

We have not done sufficient validations with recent chemistries to have a perfect answer. First it is important to distinguish detection of a modification and identification of a modification. m5C,...

Have you tried running with default parameters? The minCoverage, numWorkers and pvalue are far from what is normally tested, so it's possible you are just hitting an edge case. Also...

Score is dependent on coverage, and it isn't always possible to define a confidant cutoff. I would plot the data that you have (coverage vs score), the modified bases should...

The current model is trained on the DNA from 5 WGA bacterial samples and 7 native bacteria with well characterized RM systems and therefore know modifications. Given the limitations of...

We have been looking into this recently and have some public datasets to share: Host: ftp2.pacificbiosciences.com Username: baseMod Password: m5CControlTest The data is in the kinetic format from Sequel IIe,...

It looks like the ipd values have not been propagated from the bax.h5 files to the cmp.h5. Can you paste a copy of your pbalign command line? It's likely you...

Sorry I was editing, the --forQuiver option does not include the IPD, You can add the IPD to the pbalign command line. Or the simplest thing to do is post...

The option to pbalign is `--metrics` by default the`--forQuiver` option sets DeletionQV,DeletionTag,InsertionQV,MergeQV,SubstitutionQV, and loads the chemistry information. There are a number of ways to get to same result. I think...

When running with a case control, instead of using the `--outfile` parameter, specify the individual outputs `--gff --csv `

Unfortunately these kind of bugs are hard to diagnose, can you change the order of the contigs, to move the problem contig to the end? Then rerun, to see if...