#columns chr=7 start=8 probe=2 data=4-5 #coords=1 To specify exactly one column, use a range (e.g., 5-5) to specify the 5th column. All columns starting with this value are assumed to contain data. Note: If a single value is entered for the data column, it is interpreted as the "first" data column. Index of a probe or description column (optional)Įither a single index, or a range in the form of 5-10, of the data columns (required) Index of the end position column (optional) Index of the start position column (required) Index of the chromosome column (required) Valid keys are listed in the following table. The column directive line starts with #columns, followed by one or more column specifiers of the form key=value. To use this, include a column specifier directive at the head of the file. IGV 2.0 supports custom specification of columns for the ".igv" file format. Both deletions and amplifications can have continuous valued numbers represented by shading. Instructions are found in the Color Legends section of the user guide.įor data with negative numbers, IGV defaults to a blue-to-red scale that corresponds to copy numbers from -1.5 to 1.5. These assumptions are used to set the heatmap legend the legend can, however, be changed manually under the View> Color Legends. If it does not find negative numbers, it assumes that the values are absolute, with 2 as the center. If it finds them, it assumes that the data is log2(tumor/normal). IGV looks for the presence of negative numbers. Zero-based index: Physical positions are identified using a zero-based index.ĭisplay settings: To modify IGV's default display settings for the CN data, include a track line in the file.ĭoes IGV assume log2(ratio) or absolute values for copy number? The CN file format is described on the GenePattern web site. See the GFF3 specification, column 9 for more details.Ī CN file (.cn) is a tab-delimited text file that contains copy number data. This is not a requirement of gff3, rather required because bed files are whitespace delimited. You must URL encode spaces and other whitespace (e.g. The GFF Name property will become the display name of the feature. bed file, you can add GFF3-style attributes to the Name field (column 4) of a BED file which are displayed in the popup text. GFF tag option: By adding a #gffTags line to the beginning of a. For example, setting start-end to 1-2 describes exactly one base, the second base in the sequence.ĭisplay settings: To modify IGV's default display settings for the BED data, include a track line in the file. Zero-based index: Start and end positions are identified using a zero-based index. IGV does not currently support multiple track lines in a single BED file Tracks in the UCSC Genome Browser ( ) can be downloaded to BED files and loaded into IGV. The BED file format is described on the UCSC Genome Bioinformatics web site. For example, setting start-end to 1-2 describes two bases, the first and second in the sequence.Ī BED file (.bed) is a tab-delimited text file that defines a feature track. One-based index: Start and end positions are identified using a one-based index. For convenience, IGV equates chromosome numbers and names of the form chr# (e.g., 1 and chr1 are equivalent). SAI index is an IGV format, and it does not work with samtools or any other application.Ĭhromosome names: Chromosome names must be consistent between the selected reference genome and the SAM/BAM data files. SAM files can be sorted and indexed using igvtools. The GenePattern module for sorting and indexing is Picard.SortSam. Multiple tools are available for sorting and indexing BAM files, including igvtools, the samtools package, and in GenePattern. The index files must have the same base file name and must reside in the same directory as the file that it indexes.įor example, the index file for test-xyz.bam would be named or test-xyz.bai. A SAM index filename is created by appending. Specifically, a BAM index file should be named by appending. Indexing: IGV requires that both SAM and BAM files be sorted by position and indexed, and that the index files follow a specific naming convention. Starting with IGV 2.0.11, IUPAC ambiguity codes in BAM files are supported. īAM, rather than SAM, is the recommended format for IGV. These formats are described on the SAM Tools web site. A SAM file (.sam) is a tab-delimited text file that contains sequence alignment data. To load a set of BAM files merged into a single track see Merged BAM File.Ī BAM file (.bam) is the binary version of a SAM file.
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