Dmitry Mylarshchikov

bedtools fisher gives the same result with options `-s` or `-S`. Moreover, `-S` option requires `+` or `-` specified after it, which is not documented. Both `+` and `-` do...

Hi! I analyze ChIP-seq data between two conditions, 1 ChIP sample and 1 Input per each condition. I have some concerns about estimated extension sizes reported in *-setup.info. I obtained...

Hi! I call differentially enriched regions between two conditions: 1 ChIP sample per each and 1 Input sample per each. Besides p-values, I would like to obtain fold-change values between...

Hey! I've been running pileups, both observed and observed/expected, with `cooltools.pileup`. I noticed that obs/exp pileups are generated 20x slower than obs pileups (as for my data) when setting `nproc=8`:...

Hey! I tried to run cooltools.pileup with a custom map_functor, but it threw an error:  It seems the issue is with the `cooltools.lib.common.pool_decorator`, specifically on [this line](https://github.com/open2c/cooltools/blob/ab97a0461a9b3b642f36c7597cd17b852c075d46/cooltools/lib/common.py#L529) and the...

v.2.2.0 fails on multiple replicates of the same sample

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### Description of the bug Hey! I was running the nascent pipeline v2.2.0 on two replicates of the same sample, and encountered the following error at the step of FASTQC:...

Sample names must contain at least underscore (?)

1

### Description of the bug Hey! I was running the nascent pipeline v2.1.1 (v2.2.0 didn't work due to #) for two runs of the same sample. I encountered an error...