How to create a genome from hg19.fa file and GTF file from ensembl to be use to visualize mapped data from tophat in IGV?

Question

[Y Tb]

I want to visualize mapped data that I got from Tophat (.bam file) and I want to use the genome that I provided in Tophat command line, but I noticed that there is an option in IGV allows user to create genome form a specific reference genome. The problem I faced that when I used the default genome in IGV "hg19" some of the genes name are not found in this release that why I prefer to use the reference genome that I provided in tophat.

[Michael]

This looks like a stub question: "my data" & "it doesn't work" is not specific enough, please take a little more care about the content, you are not trying to "create" your (as in own personal) genome in IGV, are you? Will close if not improved.

Answer 1

[Ann]

If you would like to try Integrated Genome Browser, you can add a custom genome by selecting File > Open Custom Genome

For instructions, see:

https://wiki.transvar.org/pages/viewpage.action?pageId=23200542