Arthur Rand

Hello @jorisbalc, Sorry about the delay getting back. > I assume it's the G[m]NC one, though not sure why it shows up in that way. This is possible, what you...

Hello @Salvobioinfo, > However, when I used the output file to generate a density plot of the total counts at each probability level, I was surprised to find no significant...

Hello @Salvobioinfo, > (Using 0.99) Approximately 163 sites differ between KO and CTRL. Given that I have triplicates for each sample condition, I consider an editing site as valid only...

Hello @YouxinZhao, It is difficult to recommend a specific way to count methylated positions since it depends on your biological system. But with a little more information it might be...

Hello @Shians, The command should stream the output to either standard out or a file depending on what you've specified. The program tends to be write-bound, however, so what happens...

Hello @Shians, > I think ideally the write buffer should be limited in size and block processes when they try to insert while full. `--queue-size` is what you want, it...

Hello @Shians, As per the help string: ```text -q, --queue-size Number of reads that can be in memory at a time. Increasing this value will increase thread usage, at the...

Hello @SchwarzMarek, Could you try adding `--ignore-index` like this? ```bash time_format="#command: %C\nelapsed\tdata_area\ttotal_data\tmean_cpu\n%e\t%t\t%M\t%P\n"bash /usr/bin/time -o ${outdir}/test_timing.txt -f "${time_format}" \ dist_modkit_v0.4.3/modkit extract calls \ --ignore-index \ --mapped --reference ../reference.fasta \ --bgzf -t...

Hello @Seongmin-Jang-1165 Sorry for the late response. > Number of detected m6A modifications at a site/Number of transcripts for the corresponding gene Is this different than the percent methylation reported...

Hello @mbosm, As you have guessed, these psiU and m5C calls are likely errors due to their proximity to the (real) m6A base in the DRACH motif upstream. We (the...