Update authentication.qmd

Author: LeandroRitter

authentication.qmd

@@ -396,7 +396,7 @@ Typically, reads with PMD scores greater than 3 are considered to be reliably an
 As mapDamage, PMDtools can also compute deamination profile. However, the advantage of PMDtools that it can compute deamination profile for UDG / USER treated samples (with the flag *--CpG*). For this purpose, PMDtools uses only CpG sites which escape the treatment, so deamination is not gone completely and there is a chance to authenticate treated samples. Computing deamination pattern with PMDtools can be achieved with the following command line (please note that the scripts *pmdtools.0.60.py* and *plotPMD.v2.R* can be downloaded from the github repository here https://github.com/pontussk/PMDtools):
 
 ```bash
-samtools view Y.pestis_sample10.bam | pmdtools --platypus > PMDtemp.txt
+samtools view Y.pestis_sample10.bam | pmdtools --platypus > PMD_temp.txt
 ```
 
 We can then run simple R commands directly from the terminal (without loading R itself with) the following.