Paste this custom track line into the text box on the custom Like this: track type=bigGenePred name="My Big GenePred" description="A Gene Set Built from Data from My Lab" bigDataUrl= The basic version of the track line will look something Any of the track attributes will beĪvailable for use on bigBed tracks. Move the newly created bigGenePred file ( myBigGenePred.bb) to a web-accessible http, https, Utility command: bedToBigBed -as=bigGenePred.as -type=bed12+8 bigGenePred.txt chrom.sizes myBigGenePred.bb For example, the file for the hg38Īlternatively, you can use the fetchChromSizes script from theĬreate the bigGenePred file from your pre-bigGenePred file using the bedToBigBed YouĬan use the UNIX sort command to do this: sort -k1,1 -k2,2n unsorted.bed > input.bedĭownload the bedToBigBed program from theĭownload the chrom.sizes file for your assembly fromĭata set" for your organism). Your pre-bigGenePred file must be sortedįirst on the chrom field, and secondarily on the chromStart field. For example, you can use this bed12+8 input file,īigGenePred.txt. Shown above: name2, cdsStartStat, cdsEndStat, exonFrames, type, geneName, geneName2, The first 12 fields of pre-bigGenePred files are described by theĪlso contain the 8 extra fields described in the autoSql file definition Creating a bigGenePred track from a bed12+8 fileįormat your pre-bigGenePred file. The following bed12+8 is an example of a pre-bigGenePred text file in the case of hg38, the tables named wgEncodeGencodeAttrsVxx, where xx is the Gencode Version number. For most purposes, to get more information about a transcript, other tables will need to be used e.g. Used to subset for coding or non-coding genes. However, the values are not used for our display and can not be The fields cdsStartStat and cdsEndStat can have the values ('none','unk','incmpl','cmpl'). String geneName2 "Alternative/human-readable gene name" String geneName "Primary identifier for gene" Int exonFrames "Exon frame, or -1 if no frame for exon" String cdsEndStat "Status of CDS end annotation (none, unknown, incomplete, or complete)" String cdsStartStat "Status of CDS start annotation (none, unknown, incomplete, or complete)" String name2 "Alternative/human readable name" Int chromStarts "Start positions relative to chromStart" Int blockSizes "Comma separated list of block sizes" Uint reserved "RGB value (use R,G,B string in input file)" Uint thickEnd "End of where display should be thick (stop codon)" Uint thickStart "Start of where display should be thick (start codon)" String name "Name or ID of item, ideally both human-readable and unique" Uint chromEnd "End position in chromosome" Uint chromStart "Start position in chromosome" String chrom "Reference sequence chromosome or scaffold"
Is pulled in when the bedToBigBed utility is run with the Thisĭefinition, contained in the file bigGenePred.as, The following autoSql definition specifies bigGenePred gene prediction files. The hosting section of the Track Hub Help documentation. As with all big* files,īigGenePred files must be hosted on a web-accessible server (http, https, or ftp) to be displayed.įor more information on finding a hosting location for your bigGenePred files, please see
The advantage of using a binaryįormat is that only the portions of the file needed to display a particular region are read,Īllowing for much faster performance when working with large data sets. Much like bigBed, bigGenePred files are in an indexed binary format. as) file that defines the extra fields of the bigGenePred. bigGenePredįiles can be created using the program bedToBigBed, run with the -asĪutoSql (. To display start codons, stop codons, and amino acid translations.īefore compression, bigGenePred files can be described as bed12+8 files. The bigGenePred format includes 8 additional fields that contain details about codingįrames, annotation status, and other gene-specific information. GenePred text-based format supported using theīigBed format, so it can be efficiently accessed over a The bigGenePred format is a superset of the The bigGenePred format stores positional annotations for collections of exons in a compressedįormat, similar to how BED files are compressed
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