qiangfu-eu

Next we tested one human sample, I restrict the analysis only on chr1 to save time. However, here there is 6% difference between the methylation level estimated by two methods,...

I am not sure what causing such differences. As I would expect that when using the same BAM file with same setting, I should obtain similar results. What do you...

`modbam2bed` is v0.9.5 `'modkit` is v0.1.4. I have not yet updated to 0.1.5, as there is no real algorithmic changes. The log files are clean without any issues. The logs...

I rechecked `modbam2bed` generated bed file: PAI55644_EPI9.5mC.CpG.pileup.chr1.cpg.acc.bed. I noticed there are 'nan' reported. If filter out those records, the row count of bed files becomes very similar, yet still 318...

@ArtRand thanks for pointing my errors in the `awk` command. Luckily, it does NOT influence the count statistics generated. I run `--no-filtering` as requested. And the results is below. ```...

Thanks @ArtRand for checking this in detail. I will see whether I can share directly the BAM file tomorrow. I did test on human dataset. But as shown in the...

Hello, @ArtRand. You can retrieve it at https://drive.google.com/file/d/1QGUJgNZYWj1h79SLOCzsYQhwVRHckx6B/view?usp=share_link. Let me know when you download it. I just want to stress that due to short fragments sequencing, only half of the...

Exactly.

Hi, @ArtRand, thanks for the efforts. Indeed, the circular nature of plasmid could causing issues for the tool. So you mean that `modkit` and `modbam2bed` handles this differently that causes...

@ArtRand I tried the latest version. The differences are still there. One extra difference that I have overlooked previously is that `modbam2bed` always identifies more calls then `modkit`. There are...