Question: Genome name in Bam file, IGV visualization problem
gravatar for ksiusha.obraztsova
2.8 years ago by
United States
ksiusha.obraztsova0 wrote:

I am using IGV for Mac (2.3.68) to visualize the alignments I made in Galaxy against E.coli MG1655 genome. Unfortunately I am getting an error saying that genome names don't match. Both .sam and .bam files contain "chr" as a genome/sequence name and I don't know how to change it so it will match genome name in IGV (NC_00913.2). All the downstream analysis files like clued peaks in .bed and .bigwig are being loaded on to IGV but I can't see anything in the tracks. Can you suggest something?

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