Solid v dotted line in map snapgene viewer code#
To color code all bases, regardless of whether they are mismatched, right-click the track and select Show All Bases from the pop-up menu. This has the effect of de-emphasizing low quality reads. In addition, mismatched bases are assigned a transparency value proportional to the read quality known as the phred score. Insertions are indicated by a purple I ( ) and deletions are indicated with a black dash ( –). Read bases that do not match are color coded, and insertions and deletions within reads relative to the reference are marked. VCF format file displays structural variation.Ĭolors and transparency are used at two levels within alignments: (1) for mapped reads, and (2) for individual bases within reads.Ĭolor and Transparency for Individual basesīy default, read bases that match the reference are displayed in gray. IGV uses transparency to indicate quality.įor RNA-Seq, TopHat outputs separate insertions.bed and deletions.bed files which IGV will load as separate tracks. Interpreting Color by Insert Size and Interpreting Color by Pair Orientation give more detailed explaination of read colors.Īn additional factor to take into consideration when judging potential genetic alterations is quality of reads and quality of mapping. Interpretation of some of these variations are discussed briefy in this section and the next. Structural variations include insertions, deletions, inversions, tandem duplications, translocations, and other more complex rearrangements. Genetic alternations include single nucleotide variations, structural variations, and aneuploidy. IGV uses color and other visual markers to highlight potential genetic alterations in reads against a reference sequence. Enable the display of the center line by setting the Show center line property in the Alignment Preferences panel.The framed bases are the basis for Sort by operations for alignment tracks (see details below). At higher resolutions, the center line becomes two lines that frame the bases centered in the display, as shown in the figure above. When zoomed in sufficiently, IGV can display a line at the center of the display. The default visibility range threshold can be changed in the Alignment Preferences panel. When zoomed in to the alignment read visibility threshold, by default 30 KB, IGV shows the reads. For options available from the alignment track menu, including grouping, sorting and coloring options, see the alignments section of the pop-up menu page. This section gives an overview of the alignment track. In the example shown, the downsampled regions are marked by seven black rectangles just under the coverage track. The coverage track represents coverage for all the reads. Or for deep coverage, you might want to provide a smaller visibility range threshold and adjust the downsampling to show more reads.ĭownsampled reads areas are marked with a black rectangle just under the coverage track. For example, for lower coverage data, you can provide a larger visibility range threshold. You can adjust the above settings in the Alignment Preferences panel. The level of downsampling is controlled with the parameters: In areas of deep read coverage, by default the reads are downsampled, i.e. If the region is view is larger than this threshold, no alignments are visible. IGV reduces memory usage in the following two ways to improve performance of viewing alignments.Ī visibility range threshold defines the size of the region in view at which alignments are loaded. Visibility Range Threshold and Downsampling To dynamically associate coverage data with a BAM track, right-click on the coverage track and choose Load pre-computed coverage data from the pop-up menu. IGV loads this coverage track automatically when test.bam is loaded. If you need to create the index yourself, there are multiple tools available for indexing BAM files, including igvtools, the samtools package, and the Picard.SortSam module in GenePattern.įor example, the coverage track for test.bam would be named. bam file from a sequencing facility, you will usually also get the corresponding index file. When loading by file, IGV automatically searches for the index file within the same directory as the data file. When loading by URL, the URL to both the data file and the index file should be specified. For example, the index file for test-xyz.bam would be named, or alternatively test-xyz.bai. The index file should have the same filename but with the. IGV requires that BAM and CRAM files have an associated index file. Related topics on other pages cover more detailed topics:Īligned reads from sequencing can be loaded into IGV in the BAM format, SAM format, or CRAM format.īoth BAM and SAM files are described on the Samtools project page and in the 2014 article titled Sequence Alignment/Map Format Specification by the SAM/BAM Format Specification Working Group. This page introduces viewing alignment data and associated tracks in the following sections:
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