Where do I get the fasta formatted genome files?
Genomic reference sequences in the supported format can be downloaded from the UCSC Genome Bioinformatics web page. Please refer to the CASAVA User Guide, p.138, ‘Generating Reference Files’ for more instructions. Another good source of genomic sequence is NCBI. Note that the software has only been tested with Human, Mouse, and Rat genomes from these sites. Other genomes may require additional effort on the part of the user to have the data properly formatted.
Genomic reference sequences in the supported format are available from iGenome for the most common model organisms; refer to the CASAVA User Guide, ‘Generating Reference Files’ for more instructions. They can also be downloaded from the UCSC Genome Bioinformatics web page. Another good source of genomic sequence is NCBI. Note that the software has only been tested with Human, Mouse, and Rat genomes from these sites. Other genomes may require additional effort on the part of the user to have the data properly formatted. • Where do I get the files that contain exon and splice junction annotations. As of CASAVA v1.7, eland_rna uses the refFlat.txt.gz or seq_gene.md.gz file to generate the splice junction set automatically. The refFlat.txt.gz file is available from UCSC, while the seq_gene.md.gz file is from NCBI. They should be provided gzip compressed, and should be from the same build as the reference files you are using for alignment. They are available from iGenome for the most common
