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Open chromatin predict in badly aligned regions

3

Hello and thanks again for the great tool. We've run open chromatin predict and obtained bedGraphs, which we've converted to bigWigs and visualized in IGV. These look great in areas...

nchernia

Question about "skipped reads"

1

Hi, @ArtRand First, thank you for developing such a useful tool. I have a question about the definition and behavior of "skipped reads" when using the modkit extract full command....

jennyp76

Open Chromatin Predict Stuck

1

Thanks for developing this useful tool. I am having trouble on Open Chromatin Predict(modkit open-chromatin predict). The output always stop writing at some point and I receive no error message....

zhihao6201

OOM with extract calls for very large bam files

6

I'm running modkit extract calls (v0.5.0) on some very large bams on my HPC, and it seems to be failing out with an OOM even if I have 50GB of...

billytcl

how to remove DMR segment output with low percentage of samples used in statistical test

2

When calling DMRs with the `--segment` option I notice a lot of overlap in my samples between two different tests. By that I mean I looked at differential methylation across...

eesiribloom

High fail-read counts at negative-strand CpGs with Dorado 1.0.2 (5mCG) and Dorado 1.1.1(5mCG and 5mC context) but not dorado 1.0.2 (5mC model)

1

I have a PCR fragment with defined Methylation percentages. For this issue, lets focus on 0% methylated. Goal is to be able to accurately measure the input Methylation Percentage (here...

sxlaas

Test failure due to concurrency issue

2

`test_pileup_with_header` and `test_pileup_no_filt` write to the same file: https://github.com/nanoporetech/modkit/blob/8fa79e3e55c5735637f9ea3115c3e621b58fd74c/tests/test_pileup.rs#L24 https://github.com/nanoporetech/modkit/blob/8fa79e3e55c5735637f9ea3115c3e621b58fd74c/tests/test_pileup.rs#L901 Same here: https://github.com/nanoporetech/modkit/blob/8fa79e3e55c5735637f9ea3115c3e621b58fd74c/modkit/tests/test_pileup.rs#L922 This leads to test failures when tests are run in parallel. Workaround: ` cargo test --profile=release --...

Flamefire

Filtering criteria used in Modkit extract calls output

1

Hello everyone, **code used: `./modkit extract calls calls.bam calls.tsv --reference ref.fasta`** I am analyzing modification calls with Modkit. When I view my aligned BAM file in IGV, I see good...

CrisDAndres

modkit pileup produces non-deterministic results depending on thread count

2

Hello, I ran multiple replicates of the modkit pileup step using the same input BAM file and same reference genome, changing only the number of threads: Data: Same sample, same...

blipinskiaima

CRAM file as an input to modkit

6

Dear Team, Can I use "haplotagged.cram" (output of wf human variation pipeline) as an input to "modkit entropy" ?

reshu23