annotate test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report @ 6:031872f8e2e0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 14:50:31 +0000
parents dbf82dd7bdb3
children 013e53ccc7ac
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
031872f8e2e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 3
diff changeset
1 # Created with chicQualityControl version 3.6
3
dbf82dd7bdb3 "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
dbf82dd7bdb3 "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.
dbf82dd7bdb3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
4
dbf82dd7bdb3 "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
dbf82dd7bdb3 "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
dbf82dd7bdb3 "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
dbf82dd7bdb3 "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
dbf82dd7bdb3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
9
dbf82dd7bdb3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
diff changeset
10
dbf82dd7bdb3 "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.
dbf82dd7bdb3 "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.
dbf82dd7bdb3 "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.