David E. Condon

Hi Magdalena, sure, I recommend using the Defiant version from GitHub, I think that it's more updated. Different sequencing sets will have different levels of coverage, smaller/greater percent differences, the...

Hi Magdalena, sorry about that, I mean "-CpN". and yes, with the "-CpN" option, you'll be able to see single CpG/CpN changes. Let me know how it works out!

Hi Magdalena, try the "-S" option, which allows skips of low coverage, for example, "-S 1" and increment upwards. Does that give you any DMRs?

Hi Magdalena, try the "-S" option, which allows skips of low coverage, for example, "-S 1" and increment upwards. Does that give you any DMRs?

Hi Magdalena, try increasing the accepted number of skips. Also, can you show/make a plot of your coverage distribution? I'd be curious to see, I think that you likely have...

hi Jeffin, thanks for letting me know. where have you downloaded the GTF? The GTF I downloaded from refFlat on http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/ and also gencode formats. Please send me the GTF...

Hi @khl0798 this isn't one of the recognized 11 formats. It could easily be converted, however. Do you need help converting to one of these formats? I can write a...

Hi @khl0798 I'll write a script for you to convert the data by the end of the day Central Standard Time. I'll convert to input format 4.

Hi @khl0798 [make_input_format4.txt](https://github.com/hhg7/defiant/files/2730841/make_input_format4.txt) I've attached this perl script (it has to be ".txt" not ".pl" because GitHub is stupid) which will translate files from the format you gave. run it...

Hi @khl0798 try lowering the thresholds for DMRs, for example "-CpN 4" or "-P 5" or lower the coverage threshold with "-c 5" or something like that. There are many...