New Genome

[martina...@berkeley.edu]

Could "the powers that be" please please please consider uploading the latest version (or any for that matter) of the maize genome to the IGV server? My fellow lab members and I are having a very hard time creating our own genome file that IGV can display successfully. The latest Zea mays genome is version AGPv3.31 available from Ensembl at:

ftp://ftp.ensemblgenomes.org/pub/plants/release-31/fasta/zea_mays/dna/   

and the latest annotation file is a GFF3 available here: 

ftp://ftp.ensemblgenomes.org/pub/plants/release-31/gff3/zea_mays

All of the genomes on the IGV server seem to work, and I think our BAM files will align if we can just get the genome to build/load right.

Thank you!

[James Robinson]

I just added htis a “Zea mays (AGPv3.31).  BTW there are 2 other Maize assemblies already available.  

The miRNA and repeat region features were removed from the GFF due to its size.  You can load these separately using “File > Load from server…”  after loading the assembly.

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[martina...@berkeley.edu]

Thanks Jim for your speedy response! 

[Xiaofei Wang]

Is it possible to add the latest version of Maize AGPv4.37 to IGV? I can create a genome by myself but it is so hard to load it successfully (large size). So, could you update it to version 4?

Here is the links:

ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE//fasta/zea_mays/dna/

ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE//gff3/zea_mays/

Thanks a lot!

[James Robinson]

I'll put it on the list but there is a backlog now.    For a large gff file like this I reccomend that you NOT create a .genome file, its not neccessary.   Rather just load the fasta directly to define the genome.  Then download the gff file and index it, with either tabix (preferred) or igvtools.    The indexed gff can then be loaded from the file menu.

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[Xiaofei Wang]

Yes, it works. Thanks, and I appreciate you can put it on your list! Best, Xiaofei