How to load a FASTA sequence into IGV

[Jorge Gil Angeles]

Hi!

I have a FASTA sequence in a text file with the following format:

><Name of Sequence>

<Actual sequence>

How do I load it into IGV?  Do I to change the file extension like to .txt, .fa, .fasta, .fai etc?

Thank you very much!

Truly yours,

Jorge

[robin...@gmail.com]

Loading a fasta defines your reference genome, load it from the "Genomes" menu.    Fasta files must be indexed, if it's not indexed IGV will do it for you.   This can take some time, don't close the app until its finished.   The index will have a ".fai" extension. 

I suggest you give the file a ".fasta" or ".fa" extension, although this might not be strictly neccessary.  

[Jorge Gil Angeles]

Awesome!

Thank you… let me try this out.

Thanks much!

Truly yours,

Jorge

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