Documentation

[helengracehuang]

Is it possible to show more documentation on your github page? For example, the input (e.g. what is a ContactGroup object?) and output format. I am mostly wondering how it could be compatible with Aiden lab's Juicer. Thank you in advance.

[kasperdanielhansen]

Your best bet for Bioconductor packages is always to go to the Bioc landing page and find one or more vignettes. This is because the vignettes are not rendered on Github (something I would like to change, but that's how it is right now). If you look at http://bioconductor.org/packages/release/bioc/html/bnbc.html you'll see the BNBC user's guide which is viewable at

http://bioconductor.org/packages/release/bioc/vignettes/bnbc/inst/doc/bnbc.html

I am not sure this will answer your question to be honest; we have an example with cooler files but not juicer. Feel free to follow up here.

Best, Kasper

On Wed, Mar 31, 2021 at 6:07 AM Helen Huang (Xin) @.***> wrote:

Is it possible to show more documentation on your github page? For example, the input (e.g. what is a ContactGroup object?) and output format. I am mostly wondering how it could be compatible with Aiden lab's Juicer. Thank you in advance.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/hansenlab/bnbc/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABF2DHZAEXGCDG55MCQEAM3TGKNXLANCNFSM42DTUIGA .

-- Best, Kasper

[helengracehuang]

Thank you for the information. I see how I can convert .cool file to ContactGroup object. Is there an example of converting the normalized output from bnbc back to a .cool file or some other format?

[kasperdanielhansen]

We don't have such an example. The output from BNBC is pretty simple; we have bin coordinates and bin measurements, so the challenge is really to put these into a file. You can do that in two ways

1. Write a juicer or cool file directly. I am not aware of a tool which does this in R, although we have support for writing HDF5 files. I have no idea how challenging this is.
2. Write a simple bed-like text file and use existing tools to convert text file into cool/juicer.

On Wed, Mar 31, 2021 at 9:01 AM Helen Huang (Xin) @.***> wrote:

Thank you for the information. I see how I can convert .cool file to ContactGroup object. Is there an example of converting the normalized output from bnbc back to a .cool file or some other format?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/hansenlab/bnbc/issues/1#issuecomment-810825614, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABF2DH3EYKLFZ4ZISVGKS2LTGLCEFANCNFSM42DTUIGA .

-- Best, Kasper

[cafletezbrant]

Sorry, I am late to the game here. It is recommended to write the output to a BG2 (Bedgraph2) file and use cooler load (see cooler docs https://cooler.readthedocs.io/en/latest/cli.html#cooler-load). We provide a simple utility, cg2bedgraph2 (source https://github.com/hansenlab/bnbc/blob/master/R/contactGroup_utils.R#L146) to write a ContactGroup's matrices to disk in BG2 format. Please feel free to follow up if you need additional support.

Kipper

On Wed, Mar 31, 2021 at 1:31 AM Kasper Daniel Hansen < @.***> wrote:

We don't have such an example. The output from BNBC is pretty simple; we have bin coordinates and bin measurements, so the challenge is really to put these into a file. You can do that in two ways

1. Write a juicer or cool file directly. I am not aware of a tool which does this in R, although we have support for writing HDF5 files. I have no idea how challenging this is.
2. Write a simple bed-like text file and use existing tools to convert text file into cool/juicer.

On Wed, Mar 31, 2021 at 9:01 AM Helen Huang (Xin) @.***> wrote:

Thank you for the information. I see how I can convert .cool file to ContactGroup object. Is there an example of converting the normalized output from bnbc back to a .cool file or some other format?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/hansenlab/bnbc/issues/1#issuecomment-810825614, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABF2DH3EYKLFZ4ZISVGKS2LTGLCEFANCNFSM42DTUIGA

.

-- Best, Kasper

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