BED Classification

BED classification is a calculated metadata about RegionSet file that classifies RegionSet files based on the number of columns and the types of data contained within those columns.

BED classifier calculates 2 metadata fields: BED compliance and Data Format. (BED classifier tutorial can be found here: BED Classifier tutorial)

🟢 BED compliance (compliant_columns + non_compliant_columns)

BED compliance is a string that indicates the number of compliant and non-compliant columns in the BED file. It is represented as bedn+m, where n is the number of compliant columns, and m is the number of non-compliant columns. For example, bed3+0 indicates that there are 3 compliant columns and 0 non-compliant columns.

Example

bed3+0, bed7+3

Where:

• bed3+0 indicates that there are 3 compliant columns and 0 non-compliant columns.
  
• bed7+3 indicates that there are 7 compliant columns and 3 non-compliant columns.

🟢 Data formats

The data format is a string that indicates flavor of the RegionSet format. We defined the following data formats:

class DATA_FORMAT(str, Enum):
    UNKNOWN = "unknown_data_format"
    UCSC_BED = "ucsc_bed"
    UCSC_BED_RS = "ucsc_bed_rs"
    BED_LIKE = "bed_like"
    BED_LIKE_RS = "bed_like_rs"
    ENCODE_NARROWPEAK = "encode_narrowpeak"
    ENCODE_NARROWPEAK_RS = "encode_narrowpeak_rs"
    ENCODE_BROADPEAK = "encode_broadpeak"
    ENCODE_BROADPEAK_RS = "encode_broadpeak_rs"
    ENCODE_GAPPEDPEAK = "encode_gappedpeak"
    ENCODE_GAPPEDPEAK_RS = "encode_gappedpeak_rs"
    ENCODE_RNA_ELEMENTS = "encode_rna_elements"
    ENCODE_RNA_ELEMENTS_RS = "encode_rna_elements_rs"

Note

rs refers to relaxed_score which indicates that a fifth column was present where the values are integers greater than 0.
In contrast, a strict interpretation for column 5 is: A score between 0 and 1000.

• UNKNOWN

Classification was unable to determine the data format.

• UCSC_BED

Conforms to ucsc bed

• UCSC_BED_RS

Conforms to ucsc bed but with a relaxed interpretation for the fifth column.

• BED_LIKE

Data is tab delimited but contains columns that are not compliant with ucsc bed. Example: bedn+m where n are compliant columns, m are non-compliant columns and m > 0

• BED_LIKE_RS

Data is tab delimited but contains columns that are not compliant with ucsc bed but with a relaxed interpretation for the fifth column.
Example: bedn+m where n are compliant columns, m are non-compliant columns and m > 0, Column 5 = integer > 0

• ENCODE_NARROWPEAK

Conforms to ENCODE narrowPeak

• ENCODE_NARROWPEAK_RS

Conforms to ENCODE narrowPeak but with a relaxed interpretation for the fifth column.

• ENCODE_BROADPEAK

Conforms to ENCODE broadPeak

• ENCODE_BROADPEAK_RS

Conforms to ENCODE broadPeak but with a relaxed interpretation for the fifth column.

• ENCODE_GAPPEDPEAK

Conforms to ENCODE gappedPeak

• ENCODE_GAPPEDPEAK_RS

Conforms to ENCODE gappedPeak but with a relaxed interpretation for the fifth column.

• ENCODE_RNA_ELEMENTS

Conforms to ENCODE RNA elements

• ENCODE_RNA_ELEMENTS_RS

Conforms to ENCODE RNA elements but with a relaxed interpretation for the fifth column.

ℹ️ References:

• Information on various data formats can be found here: https://genome.ucsc.edu/FAQ/FAQformat.html

• Additional detailed specifications for the Browser Extensible Data (BED) format can be found here: https://samtools.github.io/hts-specs/BEDv1.pdf

• BEDBoss tutorial of bedclassifier can be found here: BED Classifier tutorial