Why is the UCSC genome browser sequence a complement of the BDGP5 sequence?
Why is the sequence shown in the UCSC genome browser a complement of the BDGP5 sequence (fasta downloads from FlyBase and ensembl)?
The fasta download from FlyBase for a particular region:
>2L:8438269..8438280 species=Dmel; strand='+'; loc=2L:8438269..8438280; CTTTCCAGCACT
The UCSC genome browser displays a sequence as follows (screen shot below):
GAAAGGTCGTGA
which is a complement of the FlyBase sequence.
The strand information is important for the analysis that I am doing so I would like to understand the discrepancy and ensure that the FlyBase sequence is indeed on the + strand. FYI, the HUMAN fasta download from biomart from ensembl and the UCSC sequence are identical.
Any help would be appreciated!
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