Question: 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?
0
gravatar for Y Tb
4.3 years ago by
Y Tb140
USA
Y Tb140 wrote:

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.

rna-seq next-gen • 2.8k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Y Tb140

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.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Michael Dondrup45k
0
gravatar for Ann
4.3 years ago by
Ann2.2k
Concord NC USA
Ann2.2k wrote:

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

ADD COMMENTlink written 4.3 years ago by Ann2.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1608 users visited in the last hour