Category

Generic


Usage

hgLoadBed database track files(s).bed


Manual

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

options:
-noSort don't sort (you better be sorting before this)
-noBinsuppress bin field
-oldTable add to existing table
-onServer This will speed things up if you're running in a directory that
the mysql server can access.
-sqlTable=table.sql Create table from .sql file
-renameSqlTable Rename table created with -sqlTable to match track
-trimSqlTableIf sqlTable has n rows, and input has m rows, only load m rows, meaning the last n-m rows in the sqlTable are optional
-type=bedN[+[P]] :
N is between 3 and 15,
optional (+) if extra "bedPlus" fields,
optional P specifies the number of extra fields. Not required, but preferred.
Examples: -type=bed6 or -type=bed6+ or -type=bed6+3
(see http://genome.ucsc.edu/FAQ/FAQformat.html#format1)
Recommended to use with -as option for better bedPlus validation.
-as=fields.asIf you have extra "bedPlus" fields, it's great to put a definition
of each field in a row in AutoSql format here.
-chromInfo=file.txt Specify chromInfo file to validate chrom names and sizes.
-tab Separate by tabs rather than space
-hasBin Input bed file starts with a bin field.
-noLoad - Do not load database and do not clean up tab files
-noHistory - Do not add history table comments (for custom tracks)
-notItemRgb - Do not parse column nine as r,g,b when commas seen (bacEnds)
-bedGraph=N - wiggle graph column N of the input file as float dataValue
- bedGraph N is typically 4: -bedGraph=4
-bedDetail - bedDetail format with id and text for hgc clicks
- requires tab and sqlTable options
-maxChromNameLength=N - specify max chromName length to avoid
- reference to chromInfo table
-tmpDir= - path to directory for creation of temporary .tab file
- which will be removed after loading
-noNameIx - no index for the name column (default creates index)
-ignoreEmpty - no error on empty input file
-noStrict - don't perform coord sanity checks
- by default we abort when: chromStart >= chromEnd
-allowStartEqualEnd - even when doing strict checks, allow
chromStart==chromEnd (zero-length e.g. insertion)
-allowNegativeScores - sql definition of score column is int, not unsigned
-customTrackLoader - turns on: -noNameIx, -noHistory, -ignoreEmpty,
-allowStartEqualEnd, -allowNegativeScores, -verbose=0
Plus, this turns on a 20 minute time-out exit.
-fillInScore=colName - if every score value is zero, then use column 'colName' to fill in the score column (from minScore-1000)
-minScore=N - minimum value for score field for -fillInScore option (default 100)
-verbose=N - verbose level for extra information to STDERR
-dotIsNull=N - if the specified field is a '.' the replace it with -1


Share your experience or ask a question