Closed canna1998 closed 11 months ago
You can do this, and many more things, by using the --track-config
option to specify your tracks rather than just listing them by file path. See the example using --track-config
option in the README. The track options are describe in the igv.js wiki. Specifically, for your case you would set samplingDepth
in an alignment track config to a very large number, for example
Example of trackConfig.json
[
{
"name": "Variants",
"url": "test/data/variants/variants.vcf.gz"
},
{
"name": "Alignments",
"url": "test/data/variants/recalibrated.bam",
"samplingDepth": 1000000,
"color": "rgb(0,150,150)"
},
{
"name": "Genes",
"type": "",
"url": "test/data/hg38/refGene.txt.gz",
"indexURL": "test/data/hg38/refGene.txt.gz.tbi"
}
]
By default, the Downsampling option is enabled in the generated html file. I have checked the previous issues, it seems that there was no downsample function before, can I turn this option off and display all reads now?