modkit

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assess the precision of the 4mC ratio

2

Hello, I am working on quantifying the ratio of 4mC in mouse samples, but I have encountered a challenge. According to public papers, 4mC is very rare in mammals. I...

hannan666666

Error during merging bedmethyl files

1

I am trying to merge two bedmethyl files, each produced from 2 different samples, using this command modkit bedmethyl merge sample_a.bed.gz sample_b.bed.gz > merged.bed I get this error error: unrecognized...

ralanany

--ref <REFERENCE_FASTA> is to select the reference genome or transcriptome

2

@rmp When I want to perform m6A analysis and use `modkit pileup` to identify methylation information, should I specify the reference genome or the reference transcriptome with the `--ref `...

Tang-pro

failed to get modbase info for record 6bcfdea5-e9eb-4fc9-a72e-81744a77df80, Skipped: AUX data not found

5

@ArtRand @rmp Hey, I received a file named pass.fq.gz, which the company called using Dorado. I then mapped the reads from the .fq.gz file to the transcriptome, when I run...

Tang-pro

Feature request

2

Hi, Awesome tool!. Could we have a feature similar to deeptols computeMatrix for creating metagene profiles of modification pattern. Thanks. Regards, Kamal

kamaloxfordpathology

FEATURE REQUEST: Extract/Calls reports number of CpG's covered in the sample

3

FEATURE REQUEST: Extract/Calls reports number of CpG's covered in the sample It would be awesome if one was using a motif file to have the percent of CpG's covered in...

ethan-mcq

Samtools code for modkit repair

1

https://nanoporetech.github.io/modkit/intro_repair.html Commands provided in link above to sort BAM files using samtools prior to repair seem to be missing 'sort': the two BAM files need to be sorted samtools -n...

sandraionescu

no m6A sites found in results

1

Hello, I am working with plant DRS dataset I ran the command (for m6A all context) $dorado basecaller rna004_130bps_sup\@v5.0.0 c6_r1/pod5/ --modified-bases-models rna004_130bps_sup\@v5.0.0_m6A\@v1/ --device cuda:all > c6_r1_sup_m6A.bam and then pileup using...

baibhav-bioinfo

Failed to read fasta index (error 2)

5

Pls look into this error and suggest how to resolve it? Here: 1. I have indexed .bam (from dorado) and then converted to fasta (reads). 2. reference: assembled (genome: NCBI)...

ramnageena11

Thank you, for the amazing tool, I have 9 bedmethyl files(4 control and 5 disease cases), these files generated from modkit tool. I have some questions

1

# 1- I want to make differential methylation anlysis between these samples, I thought I should use that command mentioned in the tutorial modkit dmr multi \ -s ${norm_pileup_1}.gz norm1...

ralanany