Loading Data and AttributesData and genomic annotations can be loaded from local files, HTTP URLs, or an IGV data server. Load from FileLoad data files by browsing for files on the local file system or other file systems you have mounted. See File Formats for information about the file formats IGV accepts. To load data from the file system:
Load from URLTo load data from an HTTP URL:
To load a file from Google Cloud Storage, enter the path to the file with the "gs://" prefix. For example, a path of gs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam will display the reads for sample NA12877 from Illumina Platinum Genomes. Notes:
Load from ServerTo load data from the IGV data server:
Removing TracksTo remove all tracks and attributes:
To remove specific tracks, do one of the following:
Creating a Chromosome Name Alias FileOne of the common causes for a data loading failure is a mismatch in chromosome names between the data file and the IGV genome it is being viewed against. Many Bowtie users report this problem after aligning to the supplied NCBI index files because chromosomes are named by accession numbers in the form: gi|224589811|ref|NC_000002.11|. The workaround is to create an alias file in 2-column tab-delimited format. The first column contains the chromosome name in your data file, for example wig or bam file. The second column contains the corresponding name in the genome assembly you are viewing (e.g., chr1 for our "hg19" genome). For instance, the alias file might look like this: NC_000002.11 <tab> gi|224589811|ref|NC_000002.11| Name the file after the genome with an underscore, the word "alias", and the extension .tab. For example, hg19_alias.tab. Place this file in the igv directory. The default location for this folder <user home>/igv/genomes, it can be changed in Preferences -> Advanced Note: Certain well-known aliases are built into IGV and do not require an alias file. These include mappings that involve adding or removing the prefix "chr" to the name, for example 1 -> chr1 and chr1 -> 1. Also, NCBI identifiers that start with "gi|" and follow the pattern illustrated in the example above are automatically mapped. |