Data Import

Loading

This section presents a summary of the data import step.

Data type Bisulfite sequencing data set
Data source /DEEP_fhgfs/data/external/blueprint/wgbs/methCalls/201609/epp_conversion/results/mergeStrandsEpp
Genome assembly used hg38
Number of samples 195
Number of sites 28806683
Detection p-values absent
coverage information is present

Sample Annotation

The loaded dataset includes a table of sample annotations describing the following traits:

No. Trait Missing Values Type
1 bedFile identifiers or text
2 sampleName identifiers or text
3 cellTypeShort categories or text
4 cellTypeGroup categories or text
5 tissueTypeShort categories or text
6 EXPERIMENT_ID identifiers or text
7 EXPERIMENT_STATUS all identical
8 STUDY_ID all identical
9 STUDY_NAME all identical
10 CENTER_NAME all identical
11 FIRST_SUBMISSION_DATE categories or text
12 SEQ_RUNS_COUNT numbers
13 SAMPLE_ID identifiers or text
14 SAMPLE_NAME identifiers or text
15 SAMPLE_STATUS all identical
16 INSTRUMENT_PLATFORM all identical
17 INSTRUMENT_MODEL all identical
18 LIBRARY_NAME identifiers or text
19 EXPERIMENT_ALIAS identifiers or text
20 LIBRARY_LAYOUT all identical
21 LIBRARY_STRATEGY all identical
22 EXPERIMENT_TYPE all identical
23 READ_STRAND all identical
24 READ_QUALITIES all identical
25 MOLECULE all identical
26 SAMPLE_ONTOLOGY_URI categories or text
27 DISEASE_ONTOLOGY_URI 111 categories or text
28 DISEASE categories or text
29 BIOMATERIAL_PROVIDER categories or text
30 BIOMATERIAL_TYPE categories or text
31 CELL_LINE all identical
32 CELL_TYPE categories or text
33 DONOR_ID categories or text
34 DONOR_AGE 3 categories or text
35 DONOR_HEALTH_STATUS 87 categories or text
36 DONOR_SEX categories or text
37 DONOR_ETHNICITY 128 categories or text
38 TISSUE_TYPE categories or text
39 TISSUE_DEPOT 10 categories or text
40 POOL_ID categories or text
41 POOLED_DONOR_IDS all identical
42 GENETIC_CHARACTERISTICS categories or text
43 TREATMENT 49 categories or text
44 TWIN_PAIR_ID all identical
45 DONOR_REGION_OF_RESIDENCE categories or text
46 SPECIMEN_PROCESSING categories or text
47 SPECIMEN_STORAGE 78 categories or text
48 SAMPLE_DESC_1 categories or text
49 SAMPLE_DESC_2 categories or text
50 SAMPLE_DESC_3 categories or text
51 bedFilename identifiers or text
52 bcfFilename identifiers or text
53 cmp_ct_mono_vs_neut 161 categories or text
54 cmp_ct_mono_vs_neut_VB 165 categories or text
55 cmp_ct_mono_vs_mf 167 categories or text
56 cmp_ct_mono_vs_mf_VB 171 categories or text
57 cmp_ct_TCD4_TN_vs_CM 189 categories or text
58 cmp_ct_TCD4_TN_vs_EM 189 categories or text
59 cmp_ct_TCD4_CM_vs_EM 191 categories or text
60 cmp_ct_TCD8_TN_vs_CM 189 categories or text
61 cmp_ct_TCD8_TN_vs_EM 189 categories or text
62 cmp_ct_TCD8_CM_vs_EM 191 categories or text
63 cmp_ct_neut_myel_vs_meta 189 categories or text
64 cmp_ct_neut_meta_vs_band 189 categories or text
65 cmp_ct_neut_band_vs_segm 189 categories or text
66 cmp_ct_neut_early_vs_mature 171 categories or text
67 Predicted Male Probability numbers or identifiers
68 Predicted Gender categories or text

The full sample annotation table is available as a comma-separated value file accompanying this report.