Mercurial > repos > bgruening > hicexplorer_hicdetectloops

annotate test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report @ 9:ffc33339cd3e draft default tip

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 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 19:28:55 +0000
parents 0410b6aada45
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
ffc33339cd3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 8
diff changeset
1 # Created with chicQualityControl version 3.7.5
3
1119cdd14ddb "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
1119cdd14ddb "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.
1119cdd14ddb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
4
1119cdd14ddb "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
1119cdd14ddb "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
1119cdd14ddb "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
1119cdd14ddb "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
1119cdd14ddb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
9
1119cdd14ddb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
10
1119cdd14ddb "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.
1119cdd14ddb "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.
1119cdd14ddb "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.