Hello Ateeq,

Custom reference genomes are loaded in FASTA format. Help for preparing the data is in our wiki:
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
http://wiki.g2.bx.psu.edu/Learn/CustomGenomes

Best,

Jen
Galaxy team

On 6/14/12 9:15 AM, Ateequr Rehman wrote:
Dear All

I am analysing bacterial RNA seq (illumina). as my reference genome is not in galaxy. so i need to downlaoded the reference genome from  NCBI and upload to my history

Should i use reference genome with  gene features or  single  fasta file with out any annotation information. even after download should i need to modify or it should be used as it is.

Thanks in advance
Ateeq




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