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Update README.md
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README reflects change in default output prefix of ChIPulate output files.
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vishakad authored Mar 26, 2019
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Expand Up @@ -205,12 +205,12 @@ To execute ```chipulate.py``` on this file with the remaining parameters set to

python3 chipulate.py -i basicExample.tsv

No output file is specified in the above syntax. When this is the case, the input file name is used as a prefix to generate the three output files described above. In this case, the files are named ```basicExample.tsv.chipulate.out``` (the main output file), ```basicExample.tsv.chipulate.out.diag_output``` (contains intermediate output from ChIPulate along with the output from the main output file) and ```basicExample.tsv.chipulate.run_info``` (contains run information about the parameters of the simulation).
No output file is specified in the above syntax. When this is the case, the input file name is used as a prefix to generate the three output files described above. In this case, the files are named ```basicExample.chipulate.out``` (the main output file), ```basicExample.chipulate.out.diag_output``` (contains intermediate output from ChIPulate along with the output from the main output file) and ```basicExample.chipulate.run_info``` (contains run information about the parameters of the simulation).


#### Main output

In a run of the command ```python3 chipulate.py -i basicExample.tsv```, the contents of ```basicExample.tsv.chipulate.out``` are ---
In a run of the command ```python3 chipulate.py -i basicExample.tsv```, the contents of ```basicExample.chipulate.out``` are ---

p_ext p_amp energy_A chip_reads unique_chip_reads control_reads unique_control_reads
0.539179 0.18 0.15 0 0 0 0
Expand All @@ -225,7 +225,7 @@ In a run of the command ```python3 chipulate.py -i basicExample.tsv```, the cont
0.578344 0.28 0.15 6 5 6 6

#### .run_info output
The information on the parameters used to generate this output are in ```basicExample.tsv.chipulate.out.run_info``` ---
The information on the parameters used to generate this output are in ```basicExample.chipulate.out.run_info``` ---

Number of cells in ChIP sample : 100000
Control cell ratio : 0.1
Expand All @@ -236,7 +236,7 @@ The information on the parameters used to generate this output are in ```basicEx
Total read count : 1000

#### .diag_output diagnostic output
The diagnostic output generated is in ```basicExample.tsv.chipulate.out.diag_output``` ---
The diagnostic output generated is in ```basicExample.chipulate.out.diag_output``` ---

name energy_A binding sequence p_occ_chip p_occ_bg chip_fragments control_fragments unique_control_reads control_reads unique_chip_reads chip_reads amp_control_fragments amp_chip_fragments ext_control_fragments ext_chip_fragments read_count_ratio
1 0.15 direct 0.9453186827840592 0.04742587317756678 94473 497 0 0 0 0 3396 2674 284 239
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