Arthur Rand
Arthur Rand
Hello @gyuhee0928, You're following the recommended strategy to extract read-level base modification calls. I would use `modkit extract calls`, which will produce an output that's easier to parse if you...
Hello @gyuhee0928, When you pass `--include-bed` to `modkit extract calls` the program will only use calls that fall within the regions provided. To do what you're looking for, first run...
Hello @gyuhee0928, Yes, use `modkit sample-probs` then you can find the bin where the percentile rank is ~10 (or just below 10). Then use the `range_start` value. Due to how...
Hello @hannan666666, That seems like quite a lot. In your command, is `${modkit_d}/${sample}.pileup.bed.gz` actually a bgzip-compressed bedMethyl file? This command expects an uncompressed bedMethyl file, in a quick test when...
Hello @hannan666666, I see, you certainly have enough compute resources. Do you have an idea for the rough "overall modification" level in your sample? You could estimate this quickly with...
Hello @ralanany, Are you looking to join the chrom name, start, stop coordinates with a table of CpG "names"? Modkit doesn't have that exact functionality, but most dataframe and spreadsheet...
Hello @ralanany, From a quick search on your CpG names, it looks like these identifiers come from an Illumina [probeset](https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=2412450825_KTajdDlXo5zGde1S9TIavp5AARK5&db=hg38&c=chr1&g=genotypeArrays). If this is the case, I would download these tables...
Hello @Raya-Faigenbaum-Romm, > I have several bam files for each sample (between 100 to 200 files). I understand that for each individual raw read a corresponding non-alignment bam file was...
Hello @Raya-Faigenbaum-Romm, Sorry about the delay. > Which value do you suggest to filter the 11th column in the awk command that you suggested? I try to understand what is...
You bet, happy to help.