read_multiqc

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R tools to read in the tidy MultiQC outputs from FastQC, FastP, and FastQScreen into a tibble

read_multiqc.R

This script takes a directory and read into the enviornment Multiqc outputs from FastQC, FastP, and FastQScreen using the following functions.

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read_multiqc_fastqc() - 3 arguments:

• PATH_MQC_FQC = the path to the directory where multiqc outputs summary statistics. No default, user must provide an argument.
• FILE1 = a file to be read in. By default this will be "multiqc_general_stats.txt". If of this file was altered FILE1 must be updated to the proper name.
• FILE2 = a file to be read in. by default this will be "multiqc_fastqc.txt". If of this file was altered FILE1 must be updated to the proper name.
• FILE3 = a file to be read in. by default this will be "mqc_fastqc_overrepresented_sequencesi_plot_1.txt". If of this file was altered FILE1 must be updated to the proper name.

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read_multiqc_fastqc2() - 2 arguments:

• PATH_MQC_FQC = the path to the directory where multiqc outputs summary statistics. No default, user must provide an argument.
• FILE1 = a file to be read in. By default this will be "multiqc_general_stats.txt". If of this file was altered FILE1 must be updated to the proper name.
• FILE2 = a file to be read in. by default this will be "multiqc_fastqc.txt". If of this file was altered FILE1 must be updated to the proper name.

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read_multiqc_fastp() - 3 arguments:

• PATH_MQC_FP = the path to the directory where multiqc outputs summary statistics. No default, user must provide an argument.
• FILE1 = a file to be read in. By default this will be "multiqc_general_stats.txt". If of this file was altered FILE1 must be updated to the proper name.
• FILE2 = a file to be read in. by default this will be "mqc_fastp_filtered_reads_plot_1.txt". If of this file was altered FILE1 must be updated to the proper name.

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read_multiqc_fastqscreen() - 2 arguments:

• PATH_MQC_FQS = the path to the directory where multiqc outputs summary statistics. No default, user must provide an argument.
• FILE1 = a file to be read in. By default this will be "multiqc_fastq_screen.txt". If of this file was altered FILE1 must be updated to the proper name.