Mercurial > repos > bgruening > hicexplorer_hicvalidatelocations

annotate test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report @ 3:bccefbea9b8d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
author iuc
date Tue, 24 Mar 2020 14:27:02 -0400
parents
children 662109a754b5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
1 # Created with chicQualityControl version 3.4.3
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
4
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
5 Number of reference points: 43
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
9
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
10
bccefbea9b8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
13 Please check the results of hicInfo to validate this for your data.