pore-c

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Hi, I have an error message while trying to convert contacts pairs to cool format with the command ``` pore_c contacts export sample1.contacts cooler sample1 --fragment-table vd.fragment.parquet --chromsizes chrom_hg19.sizes ```...

erbon7

Thanks for sharing the amazing tool that greatly simplifies Pore-C analysis! Would it be possible to add an option in the cooler export module to down-weight the pairwise interactions by...

jessakay

Bumps [dask](https://github.com/dask/dask) from 2.30.0 to 2021.10.0. Commits 97494ff bump version to 2021.10.0 ac01ddc da.store to create well-formed HighLevelGraph (#8261) 9f0f002 CI: force nightly pyarrow in the upstream build (#8281) a544670...

dependabot[bot]

Bumps [dask](https://github.com/dask/dask) from 2.30.0 to 2021.10.0. Commits 97494ff bump version to 2021.10.0 ac01ddc da.store to create well-formed HighLevelGraph (#8261) 9f0f002 CI: force nightly pyarrow in the upstream build (#8281) a544670...

dependabot[bot]

mnd file

1

Thanks a lot for the amazing software! But I've noticed a few inconsistencies using it. First of all, while you're doing mnd file, you assign pos1 and pos2 to center...

taskina-alena

eharr

multi-way contacts file

3

Hi, I was wondering if the multi-way contacts derived from the alignment file are stored in a dedicated file and if yes which one ? The "alignments.parquet" file contains only...

erbon7

Questions when exploring the align_table and pair files.

2

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",...

LIZW2019

Merging Salsa beds from multiple experiments

3

Hi Eoghan et al, After sorting out my python env issues, I've managed to successfully run Pore-C-Snakemake through to its salsa bed outputs, and it seemed to work beautifully in...

claumer

Use pyranges for overlap logic

3

Some of the overlap logic implemented in `GenomeIntervalDf` could be replaced with calls to the better documented and tested pyranges api.

eharr