A Program in R for counting tags and identification of samples using barcodes
The program works as a Rscript.
To see the possible entrances of the program, type:
Rscript script_tag_count_and_sequence_barcode_removal.R --help
The following output will be generate
Options:
-f CHARACTER, --fast=CHARACTER
A joined .fasta file [Required]
-b CHARACTER, --bar=CHARACTER
A barcode file [Required]
-t TAG, --tag=TAG
write TRUE if you want to see the header with tag pair [default= NO]
-n CHARACTER, --name=CHARACTER
write TRUE if you want to see the names with tags in the sequence [default= NO]
-h, --help
Show this help message and exit
The program needs obligatorily of a -f entrance, that is a .fasta file and the -b that is a .txt barcode file.
If only the obligated filleds be fullfilled, the program will produce 2 outputs files.
The options -t and -n are optional. If the user types YES in one (or both) of this options, one (or two) more file(s) will be created
The -i option will only change the methodology, but will not influence the amount of outputs. It may be and alternative when the processment is taking to long.
Daniel K. Morais (https://github.com/kdanielmorais)
Elcio A. O. Neto (https://github.com/ElcioNeto)