Ziming_Chen

> The demix job is also telling you there's something wrong with the base calling output Hi, Thanks for your reply. However, all the pod5 files can be successfully rebased...

> This is presumably a variant on #1020. > > Also note: you are performing barcoding twice. You only need to specify `--kit-name` to _either_ `dorado basecaller` _or_ to `dorado...

> Hi, > > I found a significant issue in the pileup file where some positions have both "+" and "-" directions. However, a specific position cannot have two A...

> Hello @SimonChen1997, > > This may happen when you have a few reads that have a mis-call at a position causing them to have a base modification call. You...

> Hello @SimonChen1997, > > Yes the `--motif` argument will work for bacterial genomes. (You may also be interested in `modkit motif search`). You can use a single base "motif"...

> Hi, > > Have you resolved the problem on "segmentation fault" ? I also got the same error information promotting "Segmentation fault (core dumped)". After checking log.txt, the program...

I also looked into the pileup bed file before subseting using this command: ``` awk -F"\t" '$10 != ($12 + $13) {print $0}' ecoli_a_2_pileup_C0.bed | head ``` while it showed:...

> You cannot filter the bedMethyl as you have done prior to using `modkit dmr`. You need to have the records for each base modification (4mC and 5mC in this...

> I would recommend using the `--ignore m` option to pileup in order to remove the 5mC calls from the pileup. thanks for reply. `--ignore m` worked. However, I had...