settings.5A_pilot.txt

[ input ]
fastq_dir = /Users/anthonyshuller/Documents/Schuller/Projects/FeBABE_Upf1_5A/Sequencing_orders/020717_5A_BABE_50bp_paired/022317_analyze5Adata/FASTQ
fastq_gz_prefixes = ["HCYVJBCXY_1_AGGTTT", "HCYVJBCXY_1_CCTGAG", "HCYVJBCXY_1_GAACCC", "HCYVJBCXY_1_TTCAGA", "HCYVJBCXY_1_TGCTGT", "HCYVJBCXY_1_ACGGTG", "HCYVJBCXY_1_CATCAC", "HCYVJBCXY_1_GTAACA", "HCYVJBCXY_1_GGATCT", "HCYVJBCXY_1_TCCGGG", "HCYVJBCXY_1_AAGCTC", "HCYVJBCXY_1_CTTAAA"]
sample_names = ["1_80S_nc_AMV", "2_80S_AMV", "3_WT5A_AMV", "4_delCys5A_AMV", "5_K48C_AMV", "6_T126C_AMV", "1_80S_nc_SSIII", "2_80S_SSIII", "3_WT5A_SSIII", "4_delCys5A_SSIII", "5_K48C_SSIII", "6_T126C_SSIII"]
paired_end = False



[ parameters ]
experiment_name = 5AFeBabe_experiment_1
read1_suffix = _1.fastq.gz
read2_suffix = _2.fastq.gz
read1_adaptor_sequence = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
read2_adaptor_sequence = ""

rrna_fasta = /Users/anthonyshuller/Documents/Schuller/Projects/FeBABE_Upf1_5A/hrf_seq/rRNA_Sequences_ucsc_20110829.txt
pymol_base_script = structure_highlighting/ban_nomenclature_S_cerevisiae_80S_PyMOL_highlighting_base.txt
pymol_base_script_colorchange = structure_highlighting/ban_nomenclature_S_cerevisiae_80S_PyMOL_colored_by_change_base.txt
make_interactive_plots = True
trim_adaptor = True
discard_untrimmed = True
min_post_adaptor_length = 20
first_base_to_keep = 8
last_base_to_keep = 100
collapse_identical_reads = False
force_read_resplit = False
force_recollapse = False
force_retrim = False
force_remapping = False
force_index_rebuild = False
force_shapemapper = False
force_recount = False

[ output ]
results_dir = /Users/anthonyshuller/Documents/Schuller/Projects/FeBABE_Upf1_5A/Sequencing_orders/020717_5A_BABE_50bp_paired/022317_analyze5Adata/Results