From a2db4cbf48fe2c3d0161426ae516633987461807 Mon Sep 17 00:00:00 2001 From: Nikolay Oskolkov Date: Mon, 29 Jul 2024 10:32:05 +0200 Subject: [PATCH] Update authentication.qmd --- authentication.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/authentication.qmd b/authentication.qmd index c63a245c..2ff305de 100644 --- a/authentication.qmd +++ b/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.