mbtools initial run about mbtools HOT 5 OPEN

On Wed, Sep 13, 2023 at 4:29 PM Jared Simpson ***@***.***> wrote: Hi @assafgrw <https://github.com/assafgrw>, ONT's bams are standard mod bams so should work. Can you share a few lines or part of the bam file with me? Jared — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHP7JFEDH47SMTYNBYI7X7LX2GYLFANCNFSM6AAAAAA4SC3KTE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

On Thu, Sep 14, 2023 at 9:27 AM Assaf Grunwald ***@***.***> wrote: On Thu, Sep 14, 2023 at 8:53 AM Assaf Grunwald ***@***.***> wrote: > Hi Jared, > > I am sharing here the first 100 lines of a sample bam file. I suspect > that there is a difference in how the modification data is stored in bam > files generated by ONT tools. > One more place I and others were facing this problem is with wgbs tool > (generating an atlas as in loyfer et al 2023): > nloyfer/wgbs_tools#48. > > Anyway, I needed mbtools to generate input for nanomix, for now I have > overcome it with modkit but still it is an interesting issue and I guess > that solving it is needed for other tools in the future. > > Assaf > > On Wed, Sep 13, 2023 at 4:29 PM Jared Simpson ***@***.***> > wrote: > >> Hi @assafgrw <https://github.com/assafgrw>, >> >> ONT's bams are standard mod bams so should work. Can you share a few >> lines or part of the bam file with me? >> >> Jared >> >> — >> Reply to this email directly, view it on GitHub >> <#5 (comment)>, or >> unsubscribe >> <https://github.com/notifications/unsubscribe-auth/AHP7JFEDH47SMTYNBYI7X7LX2GYLFANCNFSM6AAAAAA4SC3KTE> >> . >> You are receiving this because you were mentioned.Message ID: >> ***@***.***> >> >