Mercurial > repos > bgruening > hicexplorer_hicsummatrices

annotate test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report @ 25:65558d578f4f 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 79133bc3739fbcc6c2055d589679aae312161d03
author iuc
date Mon, 04 Nov 2024 23:14:27 +0000
parents 0147ee498251
children 891202c51263
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
24
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 22
diff changeset
1 # Created with chicQualityControl version 3.7.5
19
7a0ba2f585c8 "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
7a0ba2f585c8 "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.
7a0ba2f585c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
4
7a0ba2f585c8 "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
7a0ba2f585c8 "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
7a0ba2f585c8 "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
7a0ba2f585c8 "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
7a0ba2f585c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
9
7a0ba2f585c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
10
7a0ba2f585c8 "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.
7a0ba2f585c8 "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.
7a0ba2f585c8 "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.