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bedmethyl to bigWig: thread 'main' panicked at

8

Hello, modkit version: v0.4.4 I'm trying to do a Bigwig conversion, but I got an error message. thread 'main' panicked at /root/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bigtools-0.5.5/src/bbi/bbiwrite.rs:819:14: Expected to always send.: TrySendError { kind: Disconnected...

Chuang1118

Documentation for libtorch installation

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Dear ONT Team, Thank you for developing modkit. Users with Nvidia GPUs and CUDA, typically have set $LD_LIBRARY_PATH ``` $ echo $LD_LIBRARY_PATH /usr/local/cuda/lib64:/usr/local/cuda/lib64 ``` https://github.com/nanoporetech/modkit/blob/bc8a0f118e29aef0dcefdb7aa31044e343a163c9/BUILD_NOTES_tch.txt#L12 It would be better if...

SuhasSrinivasan

modkit: filtering options are not clear

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Dear ONT Team, Thank you for developing modkit. The documentation here: https://nanoporetech.github.io/modkit/advanced_usage.html and here: https://github.com/nanoporetech/modkit/blob/master/filtering.md, are not clear about the purpose for two thresholds that appear in many modkit commands...

SuhasSrinivasan

How to calculate filter thresholds from probabilities.tsv

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Hi @ArtRand , Thanks for your continuous help! I have a naive question about how to calculate filter threshold from probabilities.tsv (generated from sample-probs). In documents, it says ``` Filtering...

KunFang93

Visualization/Summarize single molecule methylation profiles

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Hello, My recent RNA004 direct RNA seq data (including two replicate samples) has done using the following: 1/ dorado basedcaller is aligned with transcript ID. 2/ Constructing bedMethyl tables by...

Chuang1118

modkit merge on empty files produces segmentation fault

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Passing bed.gz files that are made from empty beds causes a segmentation fault, latest version.

Ge0rges

Enhancement suggestion for DMR documentation

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Hi folks, I was working with `modkit dmr pair` quite a lot recently, and in the output, it seems like column 8 and column 10, sample_a total and sample_b total,...

lubitelpospat

modkit find-motifs won't accept gzipped reference genome

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`modkit find-motifs` fails if the reference genome is gzipped (see example error message below). This is inconvenient, inconsistent with dorado, which accepts a gzipped reference genome, and not clear from...

granek

Clarification about reported strand needed

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Hi folks, Thank you for developing modkit! I was playing with some human data recently, and while doing so, I noticed an unusually high number of m6A's in bedMethyl produced...

lubitelpospat

running modkit dmr after `epi2me-labs/wf-human-variation` pipeline using mod

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Hi, I ran my samples using the `epi2me-labs/wf-human-variation` pipeline using mod, and I obtained `.bedmethyl` files as the output. Now I’d like to run `modkit dmr` for differential analysis. Do...

Sepideh89