Theo Nelson comments

Results 5 comments of


                                            Theo Nelson

Could not create read group in fast5 file

P.S.: I ran `slow5tools quickcheck /content/HCV_IVT_004_ALIGNED_SIGNALS.blow5` and `slow5tools stats HCV_IVT_004_ALIGNED_SIGNALS.blow5` without issue file version 0.2.0 file format BLOW5 record compression method zlib sigal compression method svb-zd number of read groups...

Could not create read group in fast5 file

Ah I see! The file was generated by first extracting the readIDs: `slow5tools skim --rid HCV_IVT_004.blow5 > HCV_IVT_004_full_blow5_readIDs.txt` taking minimap2 generated alignments for the same file to generate common read...

Strange bias between percent_modified and valid_coverage from modkit pileup

Hi flofloflo-cell, Not the developer, but I think for this issue it would be helpful if you a.] posted the modkit filtering thresholds that were calculated and b.] run modkit...

Can dorado mistakenly identify m6A as a result of other methylation on A?

Hi Salvobioinfo, Not a developer of Dorado, but happy to add my two cents. The parameters of the experiment are key when quantifying m6a sites. To achieve robust decrease in...

Can dorado mistakenly identify m6A as a result of other methylation on A?

Dear Salvo, A thread that really helped me over in the modkit world is this one: https://github.com/nanoporetech/modkit/issues/198 As ArtRand suggests, if you run `modkit sample-probs ${modbam} --hist ${histogram_dir} --percentiles 0.1,0.8,0.85,0.9`...