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Question: position in extract full

2

I am trying to extract positions the same way as in pileup. I do this `pos = ifelse(mod_strand == ref_strand, ref_position, ifelse(ref_strand == "+", ref_position + 1, ref_position - 1))`...

privefl2

Modkit motif search

2

Hi, I'm using modkit pileup and modkit motif search with bacterial samples (DNA). I'm trying to detect m6A modifications and known motifs for my species. The problem I'm facing is...

rania-o

My graph is different from the one on the official website, is it because of smoothing? How exactly should smoothing be done?

wjj8-a

More precision on how are base modification probabilities calculated with Modkit

4

Hi, I have read the documentation on base modification probability calculation, but some points are still not completely clear to me. I would really appreciate it if you could help...

OceaneMion

Setting up a suitable value for --filter-threshold or --percentile for modkit pileup command

5

Hi Team, I basecalled my data using Dorado in Super accuracy mode for 5mC and 5hmC in CG and 6mA all context and aligned with the reference genome during basecalling....

gsukrit

Random failures in `test_repair_regression`

1

The test `test_repair_regression` fails often but not always ``` thread 'test_repair_regression' panicked at modkit/tests/test_repair.rs:63:9: assertion `left == right` failed: record 10fc76b1-f06f-42f5-9275-09cd438c1db5 not the same left: Record(tid: 3, pos: 57) right:...

Flamefire

Unexcepted output with modkit adjust-mods --convert h m

4

This is what I have for one read in the original BAM: ``` MM:Z:C+h?,3,0,0,2,1,0,9,4,4,0,2,2,1,2,3,5,0,0; C+m?,3,0,0,2,1,0,9,4,4,0,2,2,1,2,3,5,0,0; ML:B:C, 9,15,14,10,11,15, 6, 6, 7,11,16,10,10,11,11,18,16,18, 26,35,43,56,65,35,27,51,46,42,51,47,55,35,36,68,70,48 ``` This is what I get after ``` MM:Z:C+m?,3,0,0,2,1,0,9,4,4,0,2,2,1,2,3,5,0,0;...

privefl2

modkit pileup --interval-size 1000000 --chunk-size 100

1

Hello When running modkit pileup on the same BAM and reference genome, I observed output differences depending on whether interval and chunk parameters were set. Commands ``` modkit pileup modkit...

blipinskiaima

Filtering out significantly DMR sites from `modkit dmr` output.

15

@ArtRand I have two datasets - one for 5mC and one for 5mC 5hmC. I have run `modkit dmr pair` on both of them separately. For finding significantly DMR sites...

ArnavBharti

How to filter the 6mA `pileup.bed` file?

1

For 6mA site identification, is it necessary to filter the `pileup.bed` file to obtain reliable 6mA sites? If filtering is done based on `Nvalid_cov`, `percent.modified`, and `Nmod`, what would be...

yyzhou4535