ncER_datasets

• Supplementary_Table_S1_FeatureDescription_20181009.xlx contains the description and accession links of all input features used in the model. The file was created on October 10th 2018.
• xgboost_github_v1.py contains the python script used to train the XGBoost model (March 6th 2019).
• ncER version 1 (ncER_10bpBins_percentile_version1.txt.gz) contains the genome-wide percentiles (10bp bins) of the ncER scores created on August 13th 2018. The coordinates are mapped to hg19.
• ncER version2 are available in two formats:
  • Bin_1bp: 1 file per chromosome, with the 1bp resolution genome-wide percentile of the ncER scores created on March 6th 2019. The coordinates are mapped to hg19.
  • Bin_10bp: 1 file (ncER_10bpBins_allChr_coordSorted.txt.gz) with the 10bp resolution genome-wide percentile of the ncER scores created on March 6th 2019. The coordinates are mapped to hg19.

Download Links

Version	Link	Description
v1	ncER_10bpBins_percentile_version1.txt.gz	(historical) v1 - 10bp - all chromosomes
v2	ncER_10bpBins_allChr_coordSorted.txt.gz	v2 - 10bp - all chromosomes
v2	ncER_perc_chr1_coordSorted.txt.gz	v2 - 1bp - chromosome 1
v2	ncER_perc_chr2_coordSorted.txt.gz	v2 - 1bp - chromosome 2
v2	ncER_perc_chr3_coordSorted.txt.gz	v2 - 1bp - chromosome 3
v2	ncER_perc_chr4_coordSorted.txt.gz	v2 - 1bp - chromosome 4
v2	ncER_perc_chr5_coordSorted.txt.gz	v2 - 1bp - chromosome 5
v2	ncER_perc_chr6_coordSorted.txt.gz	v2 - 1bp - chromosome 6
v2	ncER_perc_chr7_coordSorted.txt.gz	v2 - 1bp - chromosome 7
v2	ncER_perc_chr8_coordSorted.txt.gz	v2 - 1bp - chromosome 8
v2	ncER_perc_chr9_coordSorted.txt.gz	v2 - 1bp - chromosome 9
v2	ncER_perc_chr10_coordSorted.txt.gz	v2 - 1bp - chromosome 10
v2	ncER_perc_chr11_coordSorted.txt.gz	v2 - 1bp - chromosome 11
v2	ncER_perc_chr12_coordSorted.txt.gz	v2 - 1bp - chromosome 12
v2	ncER_perc_chr13_coordSorted.txt.gz	v2 - 1bp - chromosome 13
v2	ncER_perc_chr14_coordSorted.txt.gz	v2 - 1bp - chromosome 14
v2	ncER_perc_chr15_coordSorted.txt.gz	v2 - 1bp - chromosome 15
v2	ncER_perc_chr16_coordSorted.txt.gz	v2 - 1bp - chromosome 16
v2	ncER_perc_chr17_coordSorted.txt.gz	v2 - 1bp - chromosome 17
v2	ncER_perc_chr18_coordSorted.txt.gz	v2 - 1bp - chromosome 18
v2	ncER_perc_chr19_coordSorted.txt.gz	v2 - 1bp - chromosome 19
v2	ncER_perc_chr20_coordSorted.txt.gz	v2 - 1bp - chromosome 20
v2	ncER_perc_chr21_coordSorted.txt.gz	v2 - 1bp - chromosome 21
v2	ncER_perc_chr22_coordSorted.txt.gz	v2 - 1bp - chromosome 22
v2	ncER_perc_chrX_coordSorted.txt.gz	v2 - 1bp - chromosome X

All ncER files have the following structure :

• Column 1 is the chromosome (autosomes and chromosome X; ordered alpha-numerically).
• Column 2 is the start position of the bin (where the first base in a chromosome is numbered 0; the start base is included)
• Column 3 is the end position of the bin (where the first base in a chromosome is numbered 0; the end base is not included)
• Column 4 is genome-wide ncER percentile. The higher the percentile, the more likely essential (in terms of regulation) the region is.