hannan666666

Unexpected 5mC calls on A bases – is this normal? Content:

2

Hi, As far as I understand, 5mC modifications should not occur on adenine (A) bases. However, I noticed entries like the following in my pileup file: 1 3234432 3234433 m,AVV,0...

calculate the 5mC signal for the CG sites in a specific region

1

The pileup.bed.gz（bedMethyl files） contains all types of modifications (CG, CH), about 39G. but I only want to calculate the 5mC signal for the CG sites in a specific region. I...

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...

Out of memory in modkit find-motifs

4

my code: $modkit find-motifs \ -i ${modkit_d}/${sample}.pileup.bed.gz \ -r ${ref} \ -o ${modkit_d}/${sample}.denovo-motifs.stats.1009533.tsv \ --threads 20 \ --min-coverage 10 \ --min-frac-mod 0.95 \ --exhaustive-seed-min-log-odds 5 \ --exhaustive-seed-len 2 \ --log...

Questions about modkit segmentation model and parameter suggestions

4

Sorry to bother you again, and thank you for your previous help. Below is my current understanding of the segmentation model — I’m not sure if it is fully correct,...

modkit summary

2

Hello, If I want to achieve higher accuracy in _modkit summary_, is it appropriate to set the --mod-thresholds values based on the basecalling model in dorado for each modification type?...