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This script runs join_paired_ends.py on data that are already demultiplexed (split up according to sample, with one sample per pair of files). 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:
If an optional –barcode_indicator file is used, it is searched for in the same manner that the paired files are searched for, so if the default “_I1_” is used, S0_L001_R1_001.fastq.gz and S0_L001_R2_001.fastq.gz would be matched up with S0_L001_I1_001.fastq.gz as the barcode indicator file.
The output directory used for each call to join_paired_ends.py uses the base name of the input read 1 fastq file (a single directory would be problematic since the output names for join_paired_ends.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_join_paired_ends.py [options]
The output of running join_paired_ends.py on many input files. See script description for more details.
Process an input folder of paired-up files (by filename, with the default _R1_ and _R2_ containing the forward and reverse reads filenames, respectively). An optional parameters file is passed with -p. This file can specify an optional parameter for join_paired_ends.py, such as: join_paired_ends:pe_join_method SeqPrep
multiple_join_paired_ends.py -i input_files -o output_folder -p qiime_parameters.txt
Process an input folder of folders (with the filenames having _forward_ and _reverse_ containing the forward and reverse read filenames, respectively). The individual folder names are included in the output folder names, but not the filenames. A matching barcode fastq file (indicated by _barcode_) is also included.
multiple_join_paired_ends.py -i input_folders -o output_folder --read1_indicator '_forward_' --read2_indicator '_reverse_' --include_input_dir_path --remove_filepath_in_name -b --barcode_indicator '_barcode_'
To see what commands would be executed by the script without actually running them, use the following command:
multiple_join_paired_ends.py -i input_files -o output_folder -w