Plots for the sanity check of MIME data, including coverage, mutation rate, etc.
Run the R script
Rscript dataSanityCheck.R <count_directory> <referenceFile> <result_directory> [<sample_sheet_file>]
withe following parameters
| parameter | type | description |
|---|---|---|
| count_directory | (string) | directory where the subdirectories of the MIMEAnTo/MIMEAn2 results are lying |
| referenceFile | (string) | reference sequence in fasta format |
| result_directory | (string) | directory to save the generated plots |
| sample_sheet_file | (string) | (optional) table with information about each sample |
The count_directory has to contain the countfiles in the subdirectories 1d and 2d. The countfiles contain the nucleotide (co-)occurrences of mapped reads, which can be inferred with the tool sam2counts. The 1d and 2d count file for the respective sample is named with the respective id/barcode:
/path/to/counts
+-- 1d
| +-- 1.txt
| +-- 2.txt
| +-- 3.txt
| +-- 4.txt
+-- 2d
| +-- 1.txt
| +-- 2.txt
| +-- 3.txt
| +-- 4.txt
The optional parameter sample_sheet_file is a semilcolon (";") separated file, with additional information about each sample. It has to contain the id or barcode in a column "Encdoding" and the actual sample name in the column "Sample". This is to show the names of the samples in the plots instead of the id.
In the result_directory several plots are saved, such as
- the coverage per position per sample
- boxplots of the mutations frequency per sample
- the mutation frequency per mutations type per position per sample
- the Shannon entropy per position per sample
- ...