Arthur Rand
Arthur Rand
Hello @ccastignani, Could you tell me how you're observing the off-by-one error? It may be an artifact of the viewer. For example, the [BED specification](https://en.wikipedia.org/wiki/BED_(file_format)) is zero-based whereas many viewers...
Hello @billytcl, There isn't a simple `modkit` command to do this, you would need to write a data frame transformation to get an aggregation of methylation percentage over read positions....
Hello @billytcl, With [modkit 0.2.3](https://github.com/nanoporetech/modkit/releases/tag/v0.2.3) you can produce a table of base modification calls at the read level with `modkit extract` using the `--read-calls ` option. Thee documentation of the...
Hello @billytcl, The command will output a row for all base modification calls in the read. There is a column called `fail` that will be true iff the `call_prob` is...
@vetmohit89 Could you tell me the version of modkit and dorado you're using? It would be good to check that the modified base tags are present in the BAM (just...
Hello @vetmohit89, It looks to me like your reads are missing modified base information. There should be `MM`, `ML`, and optionally `MN` tags present. For example:  I'd recommend re-basecalling...
Hello @vetmohit89, I tried to reproduce the problem with some internal data. Using dorado-0.5.3+d9af343. ``` ${dorado} basecaller [email protected] ${pod5} \ --modified-bases m6A_DRACH \ --max-reads 10000 \ --reference ${ref} > ${outdir}/basecalls_m6A.bam...
Hello @vetmohit89, I basecalled the pod5s you put on BOX with the following command: ```text $ dorado basecaller ${basecaller} ${pod5} \ --modified-bases m6A_DRACH \ --reference ${ref} > user_basecalls_m6A.bam ``` Then...
@vetmohit89 any luck?
@vetmohit89, the file `test_m6a_2.bam` certainly does not have any MM/ML/MN tags. Could you make sure that you are specifying the `[email protected]` basecalling model? Unfortunately, your problem seems to be upstream...