modkit

modkit copied to clipboard

how to use bedmethyl tobigwig..?

8

Hello developer!! I tried to use bedmethyl tobigwig function for m6A site visualization in IGV, but I don't know the proper input file and information. the input bedmethyl file is...

Seongmin-Jang-1165

methylation_entropy test failure

6

Hello I'm updating the build recipe for `modkit` in `EasyBuild`, and I see this test error with `0.4.4-rc1`: ``` entropy::methylation_entropy::methylation_entropy_tests::test_alphabet_info - should panic ... FAILED ``` This is with `Rust`...

verdurin

High memory usage of modkit extract full

8

I have run dorado with `m5C,inosine_m6A,pseU` and want to extract the modifications into a table. However when I run `modkit extract full` it keeps being killed for being out of...

Shians

threshold of extract call of m6A

1

Hello developer!! I ran the extract call for m6a modification analysis, but I don know how to set the threshold of Probability and base quality. is there are some standards...

Seongmin-Jang-1165

BigWig Generation Failure Using "modkit bedmethyl tobigwig" Despite Correct Sorting

2

After creating the bedmethyl file from modbam using the following command: ``` ####################################### ## 3. MODIFIED-BASE BAM TO BEDMETHYL ## ####################################### ## CPG CONTEXT ## # Extract 5mC methylation at...

lucagu1965

Differential Methylation Analysis Using MODKIT: CPM Normalization and Handling Missing Data

2

Hello, I am currently analyzing differential methylation using MODKIT and comparing results with call file-based analysis. My general strategy is as follows: For each condition, I calculate: Number of detected ...

Seongmin-Jang-1165

Validity of correlation between different RNA modification calls

3

Hello. I was reviewing some of my recent RNA004 direct RNA seq data to see what modifications I could call from them. I have six replicates here, and I called...

mbosm

Chunk process for summary and sample-prob

3

Hi @ArtRand, I was wondering if it might be possible to add chunk-based processing (similar to the pileup method) for the –no-sampling option in summary and sample-prob in the future....

KunFang93

Clarification on Interpretation of 5hmC and 5mC

7

Hello @ArtRand I have a query regarding the interpretation of the attached screenshot. Specifically, I would like clarification on the following points: In the b_counts column, for the positions: Start:...

Proy321

Coverage of modekit pileup results does not match the coverage displayed on IGV

2

Hello, I used modkit pileup with a bam basecalled with dorado model [email protected] and called for m5C, m6a, pseudou and inosine. I have two questions : - The first one...

rania-o