Is anyone aware of a script that will convert a color space fasta to a fasta file?
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One thing to keep in mind - you could convert the colors into bases, but an error in the color call would throw off all the subsequent bases after that position. It may be better to align the data in colorspace (converting the reference sequence into color space), and then finding the most parsimonious conversion of the color space reads into base space reads given the reference.
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Originally posted by brachysclereid View PostI would still like to do this. In theory those problems would result in kmers occurring only once or a few times in the data set and could be removed.
It might be possible to collapse the resulting "homoconvertamers" knowing their derivation. But it would likely be easier to just do all the analysis in color space (and take advantage of the extra error detection capabilities of color space) and do the conversion to base space as a final step.
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Phillip
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I definately agree with Phillip and BAMSeek as to the advisability of doing your work in colorspace instead of in basespace. As for your specific question, there have been several cs-to-bs converters posted on SeqAnswers. Gringer posted one recently (which I did not like). Other people have posted theirs. Search for forum for the keywords "basespace colorspace"
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