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I want to convert FASTA files to pgSNP. Ive googled high and low and cant find a way to do it. Is it even possible? Can i somehow do it with bioperl or biopython or bioruby?
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That's not a conversion, which is why google isn't giving you any results. A pgSNP format file is a text file describing variants in a genome. A fasta file is a (typically) nucleotide sequence. The sequence could be of a genome, a transcript, or even just a read (from high-throughput or even Sanger sequencing). Presumably, you need to call variants or find the differences between your fasta file(s) and the reference. If you provided more details regarding exactly what you have, someone can probably give you some hints on how to proceed. -
I have a couple of FASTA files containing sequences of different neanderthals. I want to compare the results of living people's 23andme results ( in pgSNP format ) to the neanderthal samples.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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