Mercurial > repos > bgruening > hicexplorer_hicquickqc

annotate test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report @ 6:9c5078f3926b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:08:31 +0000
parents 3175b66ea9a3
children 21d859ad4502
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9c5078f3926b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 3
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1 # Created with chicQualityControl version 3.6
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3175b66ea9a3 "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
3175b66ea9a3 "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.
3175b66ea9a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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3175b66ea9a3 "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
3175b66ea9a3 "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
3175b66ea9a3 "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
3175b66ea9a3 "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
3175b66ea9a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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3175b66ea9a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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3175b66ea9a3 "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.
3175b66ea9a3 "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.
3175b66ea9a3 "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.