What does coverage mean in IGV?

Published by Charlie Davidson on

What does coverage mean in IGV?

alignment read visibility threshold
Coverage Track. When IGV is zoomed to the alignment read visibility threshold (by default, 30 KB), the coverage track displays the depth of the reads displayed at each locus as a gray bar chart.

What is IGV used for?

IGV is a desktop application for the visualization and interactive exploration of genomic data in the context of a reference genome. A key characteristic of IGV is its focus on the integrative nature of genomic studies.

What file is IGV?

IGV supports the GFF2, GFF3 and GTF file formats.

Does IGV show all reads?

Max read count: The maximum value that can be set is 100,000 reads per window. IGV uses reservoir sampling, so that all reads are kept if the read count is less than Max read count.

What does a deletion look like in IGV?

Deletions. So in the case of a deletion, the inferred insert size is GREATER THAN the expected insert size. In IGV such an event might look like the following. Reads that are colored red have larger than expected inferred sizes, and therefore indicate possible deletions.

How do I convert genome to IGV?

Click Genomes>Create . genome File. IGV displays the a window where you enter the information. Enter an ID and a descriptive name for the genome.

What does IGV stand for?

IGV

Acronym Definition
IGV Inlet Guide Vanes
IGV Istituto di Genetica Vegetale (Italian: Institute of Vegetebal Genetics)
IGV Institut für Getreideverarbeitung Gmbh (German: Institute for Cereal Processing Ltd)
IGV Incremental Growth Vehicle

What do colors mean in IGV?

” IGV colors paired-end alignments whose inferred insert size is larger than expected or whose mate read is aligned to a different chromosome. A read with a mate aligned to a different chromosome is color-coded to identify the other chromosome.”

What does red mean in IGV?

In IGV such an event might look like the following. Reads that are colored red have larger than expected inferred sizes, and therefore indicate possible deletions.

What are GFF files?

A General Feature Format (GFF) file is a simple tab-delimited text file for describing genomic features. There are several slightly but significantly different GFF file formats. IGV supports the GFF2, GFF3 and GTF file formats.

What are GTF files?

The Gene transfer format (GTF) is a file format used to hold information about gene structure. It is a tab-delimited text format based on the general feature format (GFF), but contains some additional conventions specific to gene information.

Categories: Contributing