Which Drosophila genome data( reference genome and annotation files) do most scientists use?
We mostly use the reference from UCSC (dm6, BDGP6), and annotations from flybase: http://flybase.org
here is the reference data for fruitfly on UCSC, And I used to batch download genomes from UCSC, there is rsync service, easy to maintain the local dataset.
see here: http://hgdownload.soe.ucsc.edu/downloads.html#fruitfly
$ rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZips/ .
NCBI/Ensembl/UCSC have Fly genome versions available.
You are also going to find Fly genomes at FlyBase (parts may need a subscription).
Okay thanks. Is there a more specific link? I downloaded genome files (~23) from http://www.fruitfly.org
but it's difficult to know which is the complete genome reference ( similar to hg19.fasta).
I will use example of Ensembl but same thing for other two sites.
What about the transcriptome? For example, to align to the reference genome I would use the genome.fa and features.fa but If I want o to align to the transcriptome I would need a transcripts.fa
Thank you so much for your help!
cDNA files are here at Ensembl or these are the super-set of all transcripts coding sequences resulting from Ensembl gene predictions.
NCBI has fly transcripts here.
Probably the most comprehensive site I found:
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