Does anybody know where I could find a tool to convert a nucleotide-space sequence to a color-space sequence?
Thanks a lot in advance,
Hi,
Maybe, this two paper could help you (especially the first):
Fertil, B., Massin, M., Lespinats, S., Devic, C., Dumee, P. et Giron, A. (2005) “GENSTYLE: exploration and analysis of DNA sequences with genomic signature.” Nucleic Acids Res, Juil 2005 1;33 (Web Server issue):ws12-15.
2 Dufraigne, C., Fertil, B., Lespinats, S., Giron, A. et Deschavanne, P. (2005) “Detection and characterization of horizontal transfers in prokaryotes using genomic signature.” Nucleic Acids Res, Jan 2005 13, 33(1):e6
Why? If the original data was not collected in 2 base encoding, there is nothing at all to be gained by pseudo-converting a base space file to color space. And there is no way to truly convert a single base encoded dataset into a 2 base encoded data set - the best you could do is some sort of pseudo-conversion, but it will never be true "color space" data.
Thank you for the papers Dr Olivier Bastien
@Dr Michael B Black: I want to use cutadapt tool to filter adapter into my reads
(RNA-seq data with SOLID - color space)
I have the adapters file in fasta format (nucleotide)
so I wanted to change the format to use with cutadapt tool as he asks the adapter in the same format as csFASTA and qual files.
The documentation for cutadapt says that it will do any necessary conversion itself (https://cutadapt.readthedocs.org/en/latest/colorspace.html#ambiguity-in-colorspace)
e.g. from the manual "In colorspace mode, the adapter sequences given to the -a, -b and -g options can be given both as colors or as nucleotides. If given as nucleotides, they will automatically be converted to colorspace."
Thank you very much Dr Michael B Black.
I had read in other documentation (not the same) they require that the adapter file must be the same type with the csfasta.
Thank you again for the information. I will so used cutadapt with this file.
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