nanoporetech
modkit extract full and modkit extract calls
Hi, I would like to know the difference between "modkit extract full" and "modkit extract calls".
Hello @Flower9618,
The (new-ish) modkit extract calls produces the table that used to be modkit extract --read-calls <this_table>. In v0.4 we made this into a stand-alone command. Please find the on the extract commands here. Briefly, extract full produces a table translation of the values in the MM/ML tags. So for example, a read that has 5hmC and 5mC calls will have a probability for each in this output. On the other hand, extract calls will output the predicted modification state for each position in each read. Continuing with out example, there will only be a single record for 5hmC, 5mC, or canonical.
Can you clarify which command is the equivalent of the old modkit extract please?
@mattloose modkit extract full will produce the same default table as the versions prior to version 0.4, the documentation shows the schema of the two tables. If you were using --read-calls with an older version, you'll want modkit extract calls.
Hello @Reziya,
$ modkit extract full $bam $extract_output
Will extract 6mA calls if they are in your data. You can quickly check with modkit modbam check-tags $bam --head 1000