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I already have the genomic reference sequence that I’m planning to use. How do I tell which of the annotation files I need, refFlat.txt from UCSC or seq_gene.md from NCBI?

April 26, 2017annotation files genomic I’m planning Reference sequence UCSC

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I already have the genomic reference sequence that I’m planning to use. How do I tell which of the annotation files I need, refFlat.txt from UCSC or seq_gene.md from NCBI?

2 Answers

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It is crucial that both the sequence and the annotation files are obtained from the same source. This ensures that the chromosome names and coordinates are in sync. We strongly recommend that users download the chromosomes and the annotations together from either UCSC or NCBI.

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It is crucial that both the sequence and the annotation files are obtained from the same source. This ensures that the chromosome names and coordinates are in sync. We strongly recommend that users download the chromosomes and the annotations together from either iGenome, UCSC, or NCBI.