remove_duplicates

Uses Picard to remove duplicated reads mapped to the same place in of a reference genome during alignment, and visulizing results.

Arguments

Required arguments:

• -s , --sam: Input file folder of SAM files exported from alignment to remove duplicates reads.

Optional arguments:

• -o, out_dir: Output directory, default = current working directory.

Example usage:

$ epimapper remove_duplicates -f /Users/me/results/Epimapper/alignment/sam  -o /Users/me/results

Output

Like all the other functions in EpiMapper Python package, the function will create a main Epimapper output directiry, if it is not already present in the chosen output directory. The function will also create two additional folders, which will contain the output. Here, the “sam_duplicated_removed” directory will contain the duplicate removed sam files, and the “picard_summary” folder will contian text files for each sample with dupliaction removal statistics. These text files are used to create the “Duplication_summary.csv” located in the “summary_tables” folder. Lastly, a PNG image file containing boxplots of duplication rate, estimated libary size and number of unique fragments is created and also stored in the “summary_tabels” folder.

Epimapper
    |- alignment
    |   |- removeDuplicate
    |   |   |- sam_duplicated_removed
    |   |   |- picard_summary
    |- summary_tables
    |   |- Duplication_summary.csv
    |   |- Duplication_rate.png