bigBedNamedItems manual with usage examples

Usage

bigBedNamedItems file.bb name output.bed

Manual

This tool is part of UCSC Genome Browser's utilities.

Required Arguments

file.bb: The input bigBed file.
name: The name of the item to extract.
output.bed: The output bed file. If you want the result to be printed on the screen or your console, instead of a file, put stdout here.

Options

-nameFile: Treat the name parameter as a file full of space-delimited names.
-field=fieldName: Use index on field name, default is "name".

Examples

Retrieve an item from the input bigBed by its name

In the following example, we will extract a record named rs6657048 from the input bigBed file (dbSnp153.bb):

$ bigBedNamedItems dbSnp153.bb rs6657048 stdout
chr1    1022259    1022260    rs6657048    C    1    T,    0    12    0.0327476,0.0181309,0.030366,0.0201581,-inf,0.0262923,0.0317546,0.0127232,0.0142709,0.00997843,0.01,0.0147059,    C,C,C,C,,C,C,C,C,C,C,C,    T,T,T,T,,T,T,T,T,T,T,T,    1819    snv    clinvar,clinvarBenign,commonSome,rareSome,overlapDiffClass,    53759991835    617

Retrieve records with multiple conditions

If you want to retrieve records by more than one criteria, you can set the -nameFile option. In the following example, you can retrieve all variants with rs# IDs in file myIds.txt

bigBedNamedItems -nameFile dbSnp153.bb myIds.txt dbSnp153.myIds.bed

Retrieve records by querying a different field

By default bigBedNamedItems finds matches in the name field, if you want to query a different field, you can specify the -field option. In the following example, we will retrieve all records from the input bigBed file (ccre.bb) where the records have dELS in the field called encodeLabel:

$ bigBedNamedItems -field=encodeLabel ccre.bb dELS stdout | head
chr15    63475839    63476047    EH38E1769144    208    .    63475839    63476047    255,205,0    dELS,CTCF-bound    dELS    2.08989283126    enhD    E1769144    EH38E1769144 distal enhancer-like signature
chr15    63476209    63476559    EH38E1769145    526    .    63476209    63476559    255,205,0    dELS    dELS    5.26807680919    enhD    E1769145    EH38E1769145 distal enhancer-like signature
chr15    63476570    63476755    EH38E1769146    353    .    63476570    63476755    255,205,0    dELS,CTCF-bound    dELS    3.53008748925    enhD    E1769146    EH38E1769146 distal enhancer-like signature
chr15    63478100    63478278    EH38E1769147    255    .    63478100    63478278    255,205,0    dELS    dELS    2.55437821217    enhD    E1769147    EH38E1769147 distal enhancer-like signature
chr15    63479657    63480007    EH38E1769149    724    .    63479657    63480007    255,205,0    dELS,CTCF-bound    dELS    7.24512266895    enhD    E1769149    EH38E1769149 distal enhancer-like signature
chr15    63480513    63480686    EH38E1769150    306    .    63480513    63480686    255,205,0    dELS,CTCF-bound    dELS    3.0673872344    enhD    E1769150    EH38E1769150 distal enhancer-like signature
chr15    63480788    63481138    EH38E1769151    265    .    63480788    63481138    255,205,0    dELS,CTCF-bound    dELS    2.65695408956    enhD    E1769151    EH38E1769151 distal enhancer-like signature
chr15    63481161    63481434    EH38E1769152    480    .    63481161    63481434    255,205,0    dELS    dELS    4.80043098947    enhD    E1769152    EH38E1769152 distal enhancer-like signature
chr15    63482932    63483244    EH38E1769155    405    .    63482932    63483244    255,205,0    dELS    dELS    4.05419796646    enhD    E1769155    EH38E1769155 distal enhancer-like signature
chr15    63483521    63483693    EH38E1769156    376    .    63483521    63483693    255,205,0    dELS    dELS    3.7647196654    enhD    E1769156    EH38E1769156 distal enhancer-like signature

If you want to know all fields in a bigBed file, you can use bigBedSummary:

$ bigBedSummary -fields ccre.bb
9 bed definition fields, 15 total fields
    chrom    Reference sequence chromosome or scaffold
    chromStart    Start position of feature on chromosome
    chromEnd    End position of feature on chromosome
    name    ENCODE accession
    score    0-1000, based on Z score
    strand    n/a
    thickStart    Start position
    thickEnd    End position
    reserved    RGB Color
    ccre    ENCODE classification
    encodeLabel    ENCODE label
    zScore    Max DNase Z-score
    ucscLabel    UCSC label
    accessionLabel    Accession (abbreviated)
    description    Description for browser hover

If the field that you want to query is not indexed, you will encounter error messages like

$ bigBedNamedItems -field=encodeLabel encodeCcreCombined.bb dELS stdout | head
encodeCcreCombined.bb has no indexes

In this case, you can first convert the bigBed back to bed format with bigBedToBed and then use bedToBigBed with the -extraIndex option to add additional indexes to the bigBed file.

$ bigBedToBed encodeCcreCombined.bb enC.bed
$ bedToBigBed -tab -as=ccre.as -type=bed9+6 -extraIndex=encodeLabel enC.bed hg38.chrom.size ccre.bb

File formats this tool works with

bigBed

bigBedNamedItems

Category