In the example shown, the downsampled regions are consecutive and marked by seven black rectangles just under the coverage track. The coverage track represents coverage for all the reads. to 500.ĭownsampled reads areas are marked with a black rectangle just under the coverage track. Uncheck to turn off.Į.g., for RNA-Seq alignments that cover extended regions at low depth, increase the visibility range threshold to view alignments at wider zoom levels, e.g. Users should adjust the following default settings, tuned for DNA alignments at low coverage, for specific data types in the Alignment Preferences panel.ĭefines the nominal window size at which alignments become visible default 30 kb We present these two levers in this section together because the settings for each combine to impact IGV performance. The first occurs as the threshold zoom at which alignments become visible and the second applies to areas of deep read coverage that are downsampled. IGV reduces memory usage at two levels to improve performance. 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 you specify the location of the alignment file, IGV automatically searches for the index file within the same directory. For example, the index file for test-xyz.bam would be named, or alternatively test-xyz.bai.
bai extension and must reside in the same directory as the file that it indexes. The index file should have the same filename but with the. IGV requires that BAM files have an associated index file. The preferred file format for viewing alignments in IGV is the BAM format, a binary form of Sequence Alignment Map ( SAM) format.īesides BAM, additional supported file formats related to alignments include GOBY, VCF, PSL, BED, and TDF.įor details on viewing the older Illumina Pipeline v1.3 sorted.txt format see here.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. In addition, check Show junction track to visualize splice junctions. Adjust Alignment Preferences panel parameters for RNA-Seq data, PCR-free whole genome sequences, and other data that deviate from the breadth and depth of coverage of typical DNA alignments.įor example, before loading RNA-Seq data, increase the Visibility range threshold to 500 without affecting IGV performance as expression data typically covers ~5% of the genome and the deeper coverage is by default downsampled. Some of these preferences can be overridden on a per-track basis through pop-up menu options or by loading saved sessions.ĭefault parameters are tuned to viewing DNA alignments that typically cover the entire genome at low coverage depth and filter out marked duplicate reads. Related topics on other pages cover more detailed topics:Ĭhanges to certain display parameters in the Alignment Preferences panel should be made ahead of loading data. View as pairs, color, and split screen view Color, transparency, insertions, deletions, and sorting Overview, default coverage track, extended coverage track Preferred BAM/SAM format, other formats, and sorting & indexing This page introduces viewing alignment data and associated tracks in the following sections:
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