Thursday, July 25, 2013

Configuring an IGV Genome Server

This one consumed about 2 hours before I finally figured out the problem; it was simply a mistake in compressing the files. Thanks to Precocious Llama and another lab colleague for finding and troubleshooting the issue with me!

The Integrated Genome Viewer is a genome browser tool put out by the Broad Institute. When trying to host a genome for our lab to view, I ran into some problems. My mistake was in compressing the .genome file. What worked for me was:

Make a new directory. Copy a reference genome and GFF3 annotation to it. Use the IGV client to make the .genome file (instructions found here) from the copied reference. Decompress the resulting .genome file and configure the property.txt file (instructions found here) within. Of note, the sequenceLocation field is not a directory as stated by the instructions, but a web accessible path to the reference fasta (e.g. http://www.yoursite.com/IGV/genome/sbi1.fasta).

My issue was I kept zip compressing the directory containing the files (property.txt et al.). Instead, the zip archive needed to be made of all of the files within the directory (and renamed to id.genome as per the instructions).

Once I correctly archived the files, everything worked fine.


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