Questions when exploring the align_table and pair files.

[LIZW2019]

Hi,

Thank you so much to develop such amazing technology!

I have several questions when I explore the files.
The first one is, when I look into the file "alignment.parquet", I don't understand the column "contained_fragments", what is it? It is not equal the the fragments valid in one reads.
The second one is, I want to make sure the meaning of "DJ" "IJ" depicted in the ".pairs.catalog.yaml" file.

Look forward to your reply!

[eharr]

Hi,

Thanks for using the tool and apologies for the poor documentation, I'm close to releasing a cleaned-up version with better documentation.

The "contained_fragments" field refers to the number of restriction fragments contained entirely within a single aligned segment. Ideally this would be close to 1, but in cases where there's incomplete digestion or religation of adjacent fragments then it will be > 1.

In the pairs file DJ denotes a direct junction and IJ an indirect junction and comes from the way that we decompose multiway reads into pairwise contacts. If a Pore-C read consisted of 3 restriction fragments ordered along the read A-B-C, then A-B and B-C would be direct junctions and A-C would be an indirect junction. I hope that makes sense, I talk a bit about it in this presentation from NCM (around the 15 minute mark): https://www.youtube.com/watch?v=cOihWYW7fzI

Hope this helps.

[dexon9109]

Dear @eharr ,
Thank you for your PORE-C tool and I am looking forward to the description of the new version.
Hopefully, i want to know why the "num_pass_aligns" in [*.at.catalog.yaml] is therefore less beneficial than "num_cis_contacts" so mach .I think that CIS also needs to map, and it should not be filtered so much.Look forward to your describing in detail the filtering of this step .
P.s:I've been trying to mount with Allhic recently.

Thank u~~