Trouble loading genome fasta

[kwhig...@gmail.com]

Hello,

I'm new to IGV and I'm trying to load the gencode genome annotation (the second item on this list, unzipped ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/).  

I keep getting the error message "Unknown file type: [filelocation]/gencode34.GRCh38.p13.genome.fa.  Check file extension "  It looks like a fasta to me, which should be a recognized format.

Do you have any ideas about what I might be doing wrong?  Thank you so much!

Best,

Kate    

[James Robinson]

Are you loading it from the Genomes menu?   Fasta files are not annotation files, they define the reference sequence and should be loaded from the Genomes menu.   The first time you load it will take some time while an index is created.  

Grch38 is already included in IGV as genome "hg38".

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[kwhig...@gmail.com]

Thanks for spotting that!  I'm still running into problems, though.  I got an error message saying that the index couldn't be created (pardon me -- I don't remember the exact wording) although it does look like an fai file was generated.  I can see the uploaded genome in the genomes tab but it appears to be completely empty.

On Tuesday, July 14, 2020 at 4:58:20 PM UTC-4, James Robinson wrote:

Are you loading it from the Genomes menu?   Fasta files are not annotation files, they define the reference sequence and should be loaded from the Genomes menu.   The first time you load it will take some time while an index is created.  

Grch38 is already included in IGV as genome "hg38".

On Tue, Jul 14, 2020 at 1:43 PM <kwhig...@gmail.com> wrote:

Hello,

I'm new to IGV and I'm trying to load the gencode genome annotation (the second item on this list, unzipped ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/).  

I keep getting the error message "Unknown file type: [filelocation]/gencode34.GRCh38.p13.genome.fa.  Check file extension "  It looks like a fasta to me, which should be a recognized format.

Do you have any ideas about what I might be doing wrong?  Thank you so much!

Best,

Kate    

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[James Robinson]

The exact wording is important.   You have an "igv.log" file in an igv folder under your home directory, this should have captured the error.  Could you attach it?

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[James Robinson]

Also, is there a reason you aren't just using "hg38" from our server list?  The reference sequence is the same, unless you are interested in contigs and scaffolds.