mbtools initial run

[assafgrw]

Hi Jared and Thanks for this tools.

I am trying to clone and run it but it seems like I am missing something or that something is missing in the repo.

There is no make or bash file and simply running " mbtools reference-frequency input.bam > output.tsv"
as in the README will not do. the rm file is not excusable.

Any suggestions?

Assaf

[jts]

Apologies, I put some information here: https://github.com/jts/mbtools/tree/main#compiling

[assafgrw]

Thanks Jared,
Now its working.
However, I understood that it should work with ONT modified bams (MM ML tags). But it seems that these modifications are not recognized by mbtool, running: mbtools read-region-frequency -r '39Bisulfite.tsv' -g '/home/access/ref_genomes/hg38.fa' --cpg 'my_modified_bam.bam'

results in "Processed 1564146 reads in 44.714603338s. Mean modification frequency: NaN"

Am I missing something?

Is there a way to turn ONT modified bam into a standard modified bam?

Assaf

[jts]

Hi @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

[assafgrw]

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: ***@***.***>

[assafgrw]

Sorry I realise that the other bam file was bad.

…

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: >> ***@***.***> >> >