Mercurial > repos > bgruening > hicexplorer_hicvalidatelocations

annotate test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report @ 9:11a3385e03b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 20:09:21 +0000
parents 1d201e8378b3
children
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11a3385e03b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 8
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1 # Created with chicQualityControl version 3.7.5
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bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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2 # QC report for matrices: 0_matrix.cool 1_matrix.cool
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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3 #Sparsity threshold for rejection: sparsity <= 0.05 are rejected.
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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5 Number of reference points: 43
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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6 Number of accepted reference points: 35
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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7 Number of rejected reference points: 8
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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8 Number of faulty reference points: 0
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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11 A faulty reference point is caused by the non-presence of the chromosome in one of the given matrices.
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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12 It can also be caused by the non-presence of valid Hi-C reads in a region, especially at the chromosome ends.
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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13 Please check the results of hicInfo to validate this for your data.