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This script runs extract_barcodes.py on data that are already demultiplexed (split up according to sample, with one sample per file). The script supports the following types of input:
The script assumes that the leading/trailing characters before/after the read number indicator (see –read1_indicator) are matched between forward and reverse reads. For example:
The output directory used for each call to extract_barcodes.py uses the base name of the input read 1 fastq file (a single directory would be problematic since the output names for extract_barcodes.py can be the same for different calls). Use the parameter –include_input_dir_path to also include the input directory name in the output directory path, which may be preferable in the case of an input folder of folders, and –remove_filepath_in_name can be used in this case to prevent the input read 1 fastq file base name from being used as part of the output directory name.
Usage: multiple_extract_barcodes.py [options]
The output of running extract_barcodes.py on many input files. See script description for more details.
Process an input folder of files, with default options used for extract_barcodes.py:
multiple_extract_barcodes.py -i input_files -o output_folder
Process an input folder of folders (with the filenames having _forward_ and _reverse_ containing the forward and reverse read filenames, respectively), using the extract_barcodes.py option for paired reads. The individual folder names are included in the output folder names, but not the filenames. Note: it is important to pass the –paired_data option if paired data are to be used in the extract_barcodes.py commands. Additionally, the paired fastq file type for extract_barcodes.py is specified with a qiime_parameters.txt file (with this value specified: extract_barcodes:input_type barcode_paired_end)
multiple_extract_barcodes.py -i input_folders -o output_folder -p qiime_parameters.txt --paired_data --read1_indicator '_forward_' --read2_indicator '_reverse_' --include_input_dir_path --remove_filepath_in_name
To see what commands would be executed by the script without actually running them, use the following command:
multiple_extract_barcodes.py -i input_files -o output_folder -w