Skip to content

Update authentication.qmd #93

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Jul 29, 2024
Merged

Update authentication.qmd #93

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion authentication.qmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down