modkit

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Unclear modkit pileup `--region`

2

Hi Art, To pileup many different contigs I thought of doing `modkit pileup --region contig_1,contig_2` since the documentation says `Commas are allowed`. But that seems to not be correct? I...

Ge0rges

failed to read record from bam information, truncated record in SAM/BAM/CRAM file

10

Hello, I am trying to use the `modkit extract full` command on my data, but i only get `records failed` during processing: ``` (sturgeon) p2@p2-Precision-5860-Tower:~/tools$ modkit extract full haplotagged.cram /output/HM.txt...

ziphra

Clarification on haplotagging in modkit pileup output

1

I'm using modkit pileup to generate bedmethyl files for methylation analysis. I'm interested in understanding how haplotypes are handled in the output. Specifically, I'd like to know: 1. Does modkit...

K1999ban

Issue in Inosine detection

3

We created an ADAR KO cell line, meaning no inosine should be detected in RNA. This expectation, along with the reliability of our knockout, was confirmed by Illumina sequencing. We...

Salvobioinfo

Determining Ml score threshold for quantitative comparison of methylation levels across two datasets at the same loci

2

Hello! I am attempting to compare dna adenine methylation across two datasets at the same loci from r10.4 data we have generated in two experimental conditions. We expect the methylation...

ngamarra

Can modkit be run through epi2me labs?

1

Just a question - I know that modkit is used in some of the epi2me labs workflows - can it be run stand-alone through the epi2me-labs interface? Thanks, -Ilana

irc47

Dmr pair segment misses clearly differentially methylated region

2

I have a sample in which I know there is a hypomethylated region (chr11:2698767-2700902) in the KCNQ1OT1 gene. In IGV I can clearly see the difference in methylation between this...

Aarhus-kga

Effect size in documentation should report cond-ctrl

1

In your documentation (chapter 1.13), you have: ``` -a ${norm_pileup_1}.gz \ -a ${norm_pileup_2}.gz \ -b ${tumor_pileup_1}.gz \ -b ${tumor_pileup_2}.gz \ ``` and I've checked in another issue that you clarified...

leetaiyi

Combining 5mC with 5hmC

1

As i understood, if interested in only 5mC vs C (and not 5hmC), then collapsing is performed by splitting 5hmC probabilities equally between both states: `collapsing 'h', with 'm' and...

bopohdr

find-motifs --contig failed to parse any bedmethyl records

5

Hey @ArtRand I'm having some issue running `finds-motifs` after `merge bed`. I get: ``` _My script: Finding enriched motifs for contig contig_100009 in metagenome_assembly_ > loading references from "mags//metagenome_assembly.fna" >...

Ge0rges