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Instructions_HTSBABE.txt

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+2017-12-11Instructions to run HTS-BABE analysis:1. Create settings file using templates provided. Requires fastq directory, file prefixes, sample names, read suffixes, adaptor sequence, results directory, etc.   a. This version is not set up to use paired-end reads. Leave all fields as �False� here. 2. Using settings file, run hrf_seq_main.py as: �python hrf_seq_main.py settings.filename.txt�   a. This will create wig files for each sample that is called in the settings file, mapped to the yeast rRNA (as identified in the settings file).3. Use the wig files as input to create an MA plot in Bokeh for visual analysis as: �python hrf_seq_ratio.py numerator.wig denominator.wig output.wig output.txt output   a. This will divide the wig files at all positions to compare the variant of interest (numerator) to the control (denominator). The output will automatically open an html browser to view the MA plot in bokeh, and create a .txt file of the MA plot coordinates.   b. As an alternative you can run hrf_seq_ratio_MAplot to create a pdf version of the MA plot