Example: Groups
Example: BAT_summarize
(USAGE BAT_summarize)
Command
BAT_summarize --in1 called/S1_CG.bedgraph,called/S2_CG.bedgraph,called/S3_CG.bedgraph,called/S4_CG.bedgraph --in2 called/S5_CG.bedgraph,called/S6_CG.bedgraph,called/S7_CG.bedgraph,called/S8_CG.bedgraph --groups control,case --h1 S1,S2,S3,S4 --h2 S5,S6,S7,S8 --out data/example --cir ./circos
Output files
example_diff_control_case.bedgraph
example_diff_control_case.bw
example_mean_case.bedgraph
example_mean_case.bw
example_mean_control.bedgraph
example_mean_control.bw
example_metilene_control_case.txt
example_summary_control_case.bedgraph
example_S1.bedgraph
example_S1.bw
example_S2.bedgraph
example_S2.bw
example_S3.bedgraph
example_S3.bw
example_S4.bedgraph
example_S4.bw
example_S5.bedgraph
example_S5.bw
example_S6.bedgraph
example_S6.bw
example_S7.bedgraph
example_S7.bw
example_S8.bedgraph
example_S8.bw
circos/example.conf
circos/circos.png
circos/circos.svg
View
$ head -3 data/example_summary_control_case.bedgraph
#chrom start end control_S1 control_S2 control_S3 control_S4 case_S5 case_S6 case_S7 case_S8
chr19 9294488 9294489 0.91 0.92 0.86 0.94 0.93 0.89 0.93 0.96
chr19 9294489 9294490 0.78 0.82 0.86 0.80 0.79 0.77 0.78 0.75
$ head -3 data/example_mean_control.bedgraph
#chr start end mean_control
chr19 9294488 9294489 0.9075
chr19 9294489 9294490 0.815
$ head -3 data/example_mean_case.bedgraph
#chr start end mean_case
chr19 9294488 9294489 0.9275
chr19 9294489 9294490 0.7725
$ head -3 data/example_diff_control_case.bedgraph
#chr start end diff_control_minus_case
chr19 9294488 9294489 -0.02
chr19 9294489 9294490 0.0425
$ head -3 data/example_metilene_control_case.txt
chr pos control_S1 control_S2 control_S3 control_S4 case_S5 case_S6 case_S7 case_S8
chr19 9294489 0.91 0.92 0.86 0.94 0.93 0.89 0.93 0.96
chr19 9294490 0.78 0.82 0.86 0.80 0.79 0.77 0.78 0.75
circos/circos.png (plotted region modified)
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Example: BAT_overview
(USAGE BAT_overview)
Command
BAT_overview.R -i data/example_summary_control_case.bedgraph -o data/example_overview --groups control,case
Output file
data/example_overview.pdf
View
data/example_overview.pdf
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Example: BAT_annotation
(Go to BAT_annotation usage)
Command
BAT_annotation -b genomes/hg19/TFBS.bed -i data/example_summary_control_case.bedgraph --groups control,case -o annotation/example_TFBS
Output files
annotation/example_TFBS.txt
annotation/example_TFBS.pdf
View
$ head -3 annotation/example_TFBS.txt
chr start end identifier item count control_S1 control_S2 control_S3 control_S4 case_S5 case_S6 case_S7 case_S8 mean_control mean_case
chr19 10620780 10621150 Zeb1_1 Zeb1 11 0.0000000000 0.0000000000 0.0000000000 0.0145454545 0.0072727273 0.0036363636 0.0036363636 0.0209090909 0.0036363636 0.0088636364
chr19 10653947 10654840 Zeb1_3 Zeb1 82 0.0014634146 0.0000000000 0.0009756098 0.0013414634 0.0000000000 0.0000000000 0.0012195122 0.0007317073 0.0009451220 0.0004878049
annotation/example_TFBS.pdf
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