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In labkey_to_snakemake.py fixed the parameters so that there is 3p as well 5p polya feature for every mate, which can be matched to the -a -g -A and -G options of cutadapt depending on which is the sense or antisense mate the appropriate variable is populated and the rest of variables are filled with 'XXXXXXXXXXXX' which leads to no trimming by cutadapt. The poly-A trimming rules are fixed to contain all -a -g -A -G options.
In labkey_to_snakemake.py fixed the parameters so that there is 3p as well 5p polya feature for every mate, which can be matched to the -a -g -A and -G options of cutadapt depending on which is the sense or antisense mate the appropriate variable is populated and the rest of variables are filled with 'XXXXXXXXXXXX' which leads to no trimming by cutadapt. The poly-A trimming rules are fixed to contain all -a -g -A -G options.
