scoutzxb
commented
4 years ago Getting a totally opposite result is normal. An ABAB pattern and BABA pattern makes no difference in the likelihood value. You’ll need other information like genomic GC or gene expression, epigenetics,... to judge whether the positive values correspond to A compartment or B compartment.
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On Sep 8, 2020, at 3:32 AM, YuZhang337 notifications@github.com wrote:
Hi， When I input the same input.summary and call compartment with windowsbed files of different sizes, the generated bedgraph files have opposite positive and negative values. I would like to ask why this happens? Thank you! First, My commond line was CscoreTool1.1 mm10_windows500k.bed Input.summary Input_500k 15 1000000 the Input_500k_cscore.bedgraph shows track type="bedGraph" name="Input_500k_cscore.bedgraph" chr1 3000000 3500000 0.840631 chr1 3500000 4000000 0.768102 chr1 4000000 4500000 0.474085 chr1 4500000 5000000 -0.0416192 chr1 5000000 5500000 0.664725 chr1 5500000 6000000 0.88143 chr1 6000000 6500000 0.247688 chr1 6500000 7000000 0.810238 chr1 7000000 7500000 0.283958
Then I use the same Input.summary file and different windowsbed file, my command line was: CscoreTool1.1 /mm10_windows100k.bed Input.summary Input_100k 15 1000000 & the Input_500k_cscore.bedgraph shows track type="bedGraph" name="Input_100k_cscore.bedgraph" chr1 3000000 3100000 -0.810024 chr1 3100000 3200000 -0.849683 chr1 3200000 3300000 -0.9451 chr1 3300000 3400000 -0.815716 chr1 3400000 3500000 -0.878235 chr1 3500000 3600000 -0.773507 chr1 3600000 3700000 -0.795521 chr1 3700000 3800000 -0.8204 chr1 3800000 3900000 -0.855484 chr1 3900000 4000000 -0.777805 chr1 4000000 4100000 -0.868156 chr1 4100000 4200000 -0.707285 chr1 4200000 4300000 -0.664286 chr1 4300000 4400000 -0.352066 chr1 4400000 4500000 0.331218 chr1 4500000 4600000 -0.0429275 chr1 4600000 4700000 -0.21052 chr1 4700000 4800000 0.162653 chr1 4800000 4900000 0.483256 It is opposite to the above result I feel confused about this result and want to know how to fix it Thank You!
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YuZhang337
Hi， When I input the same input.summary and call compartment with windowsbed files of different sizes, the generated bedgraph files have opposite positive and negative values. I would like to ask why this happens? Thank you! First, My commond line was CscoreTool1.1 mm10_windows500k.bed Input.summary Input_500k 15 1000000 the Input_500k_cscore.bedgraph shows track type="bedGraph" name="Input_500k_cscore.bedgraph" chr1 3000000 3500000 0.840631 chr1 3500000 4000000 0.768102 chr1 4000000 4500000 0.474085 chr1 4500000 5000000 -0.0416192 chr1 5000000 5500000 0.664725 chr1 5500000 6000000 0.88143 chr1 6000000 6500000 0.247688 chr1 6500000 7000000 0.810238 chr1 7000000 7500000 0.283958
Then I use the same Input.summary file and different windowsbed file, my command line was: CscoreTool1.1 /mm10_windows100k.bed Input.summary Input_100k 15 1000000 & the Input_500k_cscore.bedgraph shows track type="bedGraph" name="Input_100k_cscore.bedgraph" chr1 3000000 3100000 -0.810024 chr1 3100000 3200000 -0.849683 chr1 3200000 3300000 -0.9451 chr1 3300000 3400000 -0.815716 chr1 3400000 3500000 -0.878235 chr1 3500000 3600000 -0.773507 chr1 3600000 3700000 -0.795521 chr1 3700000 3800000 -0.8204 chr1 3800000 3900000 -0.855484 chr1 3900000 4000000 -0.777805 chr1 4000000 4100000 -0.868156 chr1 4100000 4200000 -0.707285 chr1 4200000 4300000 -0.664286 chr1 4300000 4400000 -0.352066 chr1 4400000 4500000 0.331218 chr1 4500000 4600000 -0.0429275 chr1 4600000 4700000 -0.21052 chr1 4700000 4800000 0.162653 chr1 4800000 4900000 0.483256 It is opposite to the above result I feel confused about this result and want to know how to fix it Thank You!