GenPlay File Formats
From GenPlay, Einstein Genome Analyzer
Contents
.2bit format
Description
A .2bit file stores multiple DNA sequences (up to 4 Gb total) in a compact randomly-accessible format. The file contains masking information as well as the DNA itself.
The file begins with a 16-byte header containing the following fields:
- signature - the number 0x1A412743 in the architecture of the machine that created the file
- version - zero for now. Readers should abort if they see a version number higher than 0.
- sequenceCount - the number of sequences in the file.
- reserved - always zero for now
All fields are 32 bits unless noted. If the signature value is not as given, the reader program should byte-swap the signature and check if the swapped version matches. If so, all multiple-byte entities in the file will have to be byte-swapped. This enables these binary files to be used unchanged on different architectures.
The header is followed by a file index, which contains one entry for each sequence. Each index entry contains three fields:
- nameSize - a byte containing the length of the name field
- name - the sequence name itself, of variable length depending on nameSize
- offset - the 32-bit offset of the sequence data relative to the start of the file
The index is followed by the sequence records, which contain nine fields:
- dnaSize - number of bases of DNA in the sequence
- nBlockCount - the number of blocks of Ns in the file (representing unknown sequence)
- nBlockStarts - the starting position for each block of Ns
- nBlockSizes - the size of each block of Ns
- maskBlockCount - the number of masked (lower-case) blocks
- maskBlockStarts - the starting position for each masked block
- maskBlockSizes - the size of each masked block
- reserved - always zero for now
- packedDna - the DNA packed to two bits per base, represented as so: T - 00, C - 01, A - 10, G - 11.
The first base is in the most significant 2-bit byte; the last base is in the least significant 2 bits. For example, the sequence TCAG is represented as 00011011. The packedDna field is padded with 0 bits as necessary to take an even multiple of 32 bits in the file, which improves I/O performance on some machines.
Usage
The .2bit files can be loaded as sequence tracks.
To be loaded the file need to have a '.2bit' extension.
BAM / SAM format
Description
SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
BAM is a Binary version of the Sequence Alignment / Map (SAM) format.
More information about these file formats can be found here
Usage
SAM files can generate fixed window track. BAM can't be used directly with GenPlay but can be easily converted in a SAM file using tools available on the Internet.
To be loaded a SAM file needs either to have a '.sam' extension or to have the following first line:
track type=sam
BED format
Description
BED format has three necessary fields and nine additional optional fields. The number of fields per line have to be constant throughout any single set of data in an annotation track. The order of the optional fields requires that lower-numbered fields be filled if higher-numbered fields are used.
- The first three required BED fields are:
- chromosome - The name of the chromosome (e.g. chr1, chrX etc.) or scaffold (e.g. scaffold10461).
- Start - The beginning position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
- End - The ending position of the feature in the chromosome or scaffold.
- The 9 additional optional BED fields are:
- name – This is the name of the gene.
- score - A score between 0 and 1000.
- strand - Defines the strand as either '+' (red) or '-' (blue).
- thickStart
- thickEnd
- itemRgb
- blockCount
- blockSizes
- blockStarts
Example
Here is an example of a bed file.
track type=bed searchURL="http://genome.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&db=hg19&hgg_gene=" chr1 11873 14409 uc001aaa.3 0 + 11873 11873 0 3 354,109,1189, 0,739,1347, chr1 11873 14409 uc010nxq.1 0 + 12189 13639 0 3 354,127,1007, 0,721,1529, chr1 11873 14409 uc010nxr.1 0 + 11873 11873 0 3 354,52,1189, 0,772,1347, chr1 14362 16765 uc009vis.2 0 - 14362 14362 0 4 467,69,147,159, 0,607,1433,2244,
Note: The search URL "http://genome.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&db=hg19&hgg_gene=" is included at the beginning of each BED file. It provides the URL that contains the description of the genes. One can form the complete URL by appending the name of the gene at the end of the search URL after the equal to sign. For example, "http://genome.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&db=hg19&hgg_gene=uc001aaa.3" will provide information on WDR 78.
Usage
A Bed file with the 3 required fields can generate stripes. If the 2 first required fields are specified, the file can be loaded as a fixed windows, a variable windows or a repeat track. If all the fields are specified the file can be loaded as a gene track.
To be loaded a Bed file needs either to have a '.bed' extension or to have the following first line:
track type=bed
BedGraph format
Description
The BedGraph format is a really simple format useful to visualize windows on the genome. This windows can have a score. The fields in a BedGraph file are the followings:
- Chromosome
- Window start position
- Window stop position
- Score
Example
track type =bedgraph chr1 18598 19673 1 chr1 124987 125426 3 chr1 317653 318092 15 chr1 427014 428027 8
Usage
BedGraph files can be used to load fixed windows and variable windows track.
They can also be loaded as stripes
A valid BedGraph file needs either to have a '.bgr' extension or to have the following first line:
track type=bedgraph
GdpGene format
Description
The GdpGene file format is used to store informations about genes. It is different than the BED format because it can store one score per exon.
The 7 mandatory fields of a GdpGene are:
- name
- chromosome
- strand
- start
- stop
- exon starts (list of the exon start positions separated by commas and with no spaces or tabulations)
- exon stops (list of the exon stop positions separated by commas and with no spaces or tabulations)
There is also an optional field:
- exon scores (list of the exon scores separated by commas and with no spaces or tabulations)
Example
Here is an example of a GdpGene file:
track type=GdpGene name=Genes_Mouse_RefSeq_07-2007.txt Xkr4 chr1 - 3204562 3661579 3204562,3411782,3660632 3207049,3411982,3661579 Rp1 chr1 - 4334223 4350473 4334223,4341990,4342282,4350280 4340172,4342162,4342918,4350473 Mrpl15 chr1 - 4764014 4775768 4764014,4767605,4772648,4774031,4775653
Note: you can add a searchURL line to the GdpGene file. It works the same way as for a BED file, described here
Usage
GFF format
Description
GFF stands for General Feature Format. They have 9 compulsory fields which are tab delimited. They are as follows:
- seqname - The name of the sequence. Must be a chromosome.
- source - The source code that was responsible for generation of this feature.
- feature - The name of this type of feature.
- start - The starting position of the feature in the sequence. The first base are 1 indexed.
- end - The ending position of the feature (inclusive).
- score - A score between 0 and 1000.
- strand - Valid entries include '+', '-', or '.' (for don't know/don't care).
- frame – Is a number between 0 and 2, if the feature is a coding exon and if the feature is not a coding exon, it is ‘.’.
- group - Lines belonging to the same group are linked together into a single item.
More information about this format can be found on Sanger website
Usage
GFF files can be used to load repeats, variable and fixed windows track as well as stripes.
A GFF file needs to have a gff extension or to have the following first line:
##GFF
GTF format
Description
GTF stands for Gene Transfer Format and is a stricter version of GFF. The first 8 GTF fields are the same as GFF. The group field has been expanded into a list of attributes. Each attribute is a type/value pair. Attributes must be terminated by a semi-colon. The gap between any two attributes must be exactly one space. The attribute list must begin with the two required attributes:
- gene_id value - A GUID for the genomic source of the sequence
- transcript_id value - A GUID for the predicted transcript
Refer to the Sanger website for further information.
Usage
Stripes, fixed and variable windows, repeat and gene tracks can be generated from a GTF file.
A GTF files must either have a '.gtf' extension or to have the following first line:
##GTF
Pair format
Description
Usage
PSL format
Description
PSL lines represent alignments, and are typically taken from files generated by BLAT or psLayout. All of the following fields are required on each data line within a PSL file:
- matches - Number of bases that match that aren’t repeats
- mismatches - Number of bases that don't match
- repeats - Number of bases that match but are part of repeats
- nbasecount - Number of 'N' bases
- numofinsertsquery - Number of inserts in query
- numofbaseinsertsquery - Number of bases inserted in query
- numofinsertstarget - Number of inserts in target
- numofbaseinsertsquery - Number of bases inserted in target
- strand - '+' or '-' for query strand. For translated alignments, second '+'or '-' is for genomic strand
- queryseqname - Query sequence name
- queryseqize - Query sequence size
- querystart - Alignment start position in query
- queryend - Alignment end position in query
- targetseqname - Target sequence name
- targetseqsize - Target sequence size
- targetstart - Alignment start position in target
- targetend - Alignment end position in target
- blockcount - Number of blocks in the alignment (a block contains no gaps)
- blocksizes - Comma-separated list of sizes of each block
- querystarts - Comma-separated list of starting positions of each block in query
- targetstarts - Comma-separated list of starting positions of each block in target
Usage
A PSL file can generate stripes. It can also be loaded as a fixed windows, a variable windows, a gene or a repeat track.
To be loaded a PSL file needs either to have a '.psl' extension or to have the following first line:
track type=psl
SOAPsnp format
Description
The SOAPsnp files contain the result of a resequencing utility that can assemble consensus sequence for the genome of a newly sequenced individual based on the alignment of raw sequencing reads on a known reference. The SNPs can then be identified on the consensus sequence through the comparison with the reference. More information about this file format can be found here
The result of SOAPsnp has 17 columns:
- Chromosome ID
- Coordinate on chromosome, start from 1
- Reference genotype
- Consensus genotype
- Quality score of consensus genotype
- Best base
- Average quality score of best base
- Count of uniquely mapped best base
- Count of all mapped best base
- Second best bases
- Average quality score of second best base
- Count of uniquely mapped second best base
- Count of all mapped second best base
- Sequencing depth of the site
- Rank sum test p_value
- Average copy number of nearby region
- Whether the site is a dbSNP.
Usage
The SOAPsnp files can be used to generate SNPs tracks. Be sure that the file has the following first line:
track type=SOAPsnp
WIG format
Description
Wiggle format (WIG) allows the display of continuous-valued data in a track format. Please refer to this page for the whole description of a wiggle file.
General Structure
Wiggle format is line-oriented. For wiggle custom tracks, the first line must be a track definition line, which designates the track as a wiggle track and adds a number of options for controlling the default display.
Wiggle format is composed of declaration lines and data lines. There are two options for formatting wiggle data: variableStep and fixedStep. These formats were developed to allow the file to be written as compactly as possible.
- variableStep is for data with irregular intervals between new data points and is the more commonly used wiggle format. It begins with a declaration line and is followed by two columns containing chromosome positions and data values:
variableStep chrom=chrN [span=windowSize] chromStartA dataValueA chromStartB dataValueB ... etc ... ... etc ...
The declaration line starts with the word variableStep and is followed by a specification for a chromosome. The optional span parameter (default: span=1) allows data composed of contiguous runs of bases with the same data value to be specified more succinctly. The span begins at each chromosome position specified and indicates the number of bases that data value should cover.
For example, this variableStep specification:
variableStep chrom=chr2 300701 12.5 300702 12.5 300703 12.5 300704 12.5 300705 12.5
is equivalent to:
variableStep chrom=chr2 span=5 300701 12.5
Both versions display a value of 12.5 at position 300701-300705 on chromosome 2.
- fixedStep is for data with regular intervals between new data values and is the more compact wiggle format. It begins with a declaration line and is followed by a single column of data values:
fixedStep chrom=chrN start=position step=stepInterval [span=windowSize] dataValue1 dataValue2 ... etc ...
The declaration line starts with the word fixedStep and includes specifications for chromosome, start coordinate, and step size. The span specification has the same meaning as in variableStep format.
For example, this fixedStep specification:
fixedStep chrom=chr3 start=400601 step=100 11 22 33
displays the values 11, 22, and 33 as single-base regions on chromosome 3 at positions 400601, 400701, and 400801, respectively.
Adding span=5 to the declaration line:
fixedStep chrom=chr3 start=400601 step=100 span=5 11 22 33
causes the values 11, 22, and 33 to be displayed as 5-base regions on chromosome 3 at positions 400601-400605, 400701-400705, and 400801-400805, respectively.
Note that for both variableStep and fixedStep formats, the same span must be used throughout the dataset. If no span is specified, the default span of one is used.
Usage
A wiggle file can generate fixed or variable windows tracks as well as stripes.
Be sure that the file extension is .wig or that the file has the following first line:
track type=wiggle