Tweet
Is anyone aware of a script that will convert a color space fasta to a fasta file?
-
-
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. -
csfasta to fasta
I 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.
Does such a script exist?Comment
-
you should use encodeFasta.py script in corona from SOLiD.Comment
-
Alas, no. Without knowing the base n-1, there are 4 base space sequences that may derive from a color space sequence starting at base n. One of those base space sequences is correct, the other 3 are incorrect. The result is that any error at any position sends one down the incorrect path. However, these will not create wildly divergent kmers because there are only 3 of them.Originally posted by brachysclereid View Post
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.
--
PhillipComment
-
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"Comment
-
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM -
Studying ecosystems means dealing with complex, multi-species communities that are hard to observe at scale. This complexity, however, hides many important questions to be answered, from how biogeochemical cycles work and how climate change can affect species distribution to how conservation strategies can work best.
Genomics, particularly since the expansion of NGS, has transformed ecosystem ecology. By sequencing environmental DNA, we can now assess biodiversity without direct...05-06-2026, 09:04 AM
Comment