notebook.community

Edit and run



In [1]:

    
r_enz= 'HindIII'



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from pytadbit.mapping.full_mapper import full_mapping



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full_mapping('/media/storage/db/reference_genome/Homo_sapiens/hg38/hg38.gem',
            nthreads=2, clean=True, r_enz=r_enz
            frag_map=False,
            out_map_dir='results/{0}/01_mapping/map{0}_r1'.format(r_enz),
            fastq_path='/media/storage/FASTQs/K562_{0}_1.fastq'.format(r_enz),
            windows=((1, 25),(1, 30),(1,50),(1,75)))



In [ ]:

    
full_mapping('/media/storage/db/reference_genome/Homo_sapiens/hg38/hg38.gem',
            nthreads=2, clean=True, r_enz=r_enz,
            frag_map=False,
            out_map_dir='results/{0}/01_mapping/map{0}_r2'.format(r_enz),
            fastq_path='/media/storage/FASTQs/K562_{0}_2.fastq'.format(r_enz),
            windows=((1, 25),(1, 30),(1,50),(1,75)))

!mkdir -p results



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!rm -rf results/HindIII/02_mapping



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!rm -rf results/MboI/02_mapping



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!pwd









    



/media/storage/Notebooks2/deo



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!head results/HindIII/01_mapping/mapHindIII_r1/K562_HindIII_1_frag_1-end.map









    



NS500645:59:HCL32BGXY:1:11101:14163:1054~2~	AAGCTTCAAGGAAATACATTT	HHHHHHEEEEEEAAEE</EEE	1	chr2:+:62077808:21
NS500645:59:HCL32BGXY:1:11101:4416:1054~2~	AAGCTTCCATTCNTTTGCTTCTGTTGTGTGTTTTTTCTTTTGTTTTTTTTTTGTTTTGGTT	HHHHHHAEEEE/#EEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEE/<EEEEEAE	0:0:1:0	chr16:+:81452828:12T45T2
NS500645:59:HCL32BGXY:1:11101:16360:1056	CGCCTNTCTCCGAGGCCCTGTATTCTGGAATCTTGTGGCTCTCTCTTGGATCCTAAGCTT	AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEHHHHHH	0:1:0	chr2:-:6811943:5C54
NS500645:59:HCL32BGXY:1:11101:17064:1056	CATCANTAACTGTATCCAAAAGGAGACGCTGCTTGGGGTGTACCCAGAGAAAACACCAAGCTT	AAAAA#EEEEEEEEEEEEEEEEEEEEE<EEEAEEEEEEEEEEEEAEEEEEEEEEEEEHHHHHH	0:1:0	chr4:-:40244040:5A57
NS500645:59:HCL32BGXY:1:11101:15358:1057	AGAAANTTCTACAGACTCCAGAGTGAAGCTT	AAAAA#EEEEEEEEEEEEEEEEEEEHHHHHH	0:1	chr2:-:89284133:5C25
NS500645:59:HCL32BGXY:1:11101:15358:1057~2~	AAGCTTAAAAGATTCACCAATTACTTGAAAATGTTTGTGCATGTGT	HHHHHHEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE	1	chr2:-:58688377:46
NS500645:59:HCL32BGXY:1:11101:22546:1059	AGCTTNATCATTTCTAGCTTTTGAGGAAAACTGGGAGACATGCGACTGCTCCTTTCACTTGAAAGCTT	AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEHHHHHH	0:1:0	chr14:-:54128571:5A62
NS500645:59:HCL32BGXY:1:11101:6478:1064~2~	AAGCTTCCATTTTATTGAAGTAGTGCACAAAGCTTTCCCTCTTATTGAGGGATTTCTTCA	HHHHHHEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE<EEEEEEEEEEE	1	chr1:-:118273696:60
NS500645:59:HCL32BGXY:1:11101:25274:1064~2~	AAGCTTTTCAAAACAAAATTAGCTCTTTCAGAATTAAGGCCTTGTTCTCTACAGAGTT	HHHHHHEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEE	1	chrX:-:81223467:58
NS500645:59:HCL32BGXY:1:11101:18285:1064	CCCTGNGTTCCTCTGCCTTTCCGGGACAGGGGGGAAGATAAGATTTCATCATGAGAAAGCTT	AAAAA#EEEAEEEEEAEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEHHHHHH	0:1:0	chr16:+:23130111:5T56



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