Hi all, In the SOLiD system, read are mapped a color-space encoded version of the reference sequence in question, after which start and end coordinates are reported. Base-space sequence can then (if needed) be extracted from the reference sequence using the given coordinates.
There is a "double encoding"-system, where the colors (0, 1, 2, 3) are changed to letters (A, C, G, T) to trick certain software to work with SOLiD data. This does not correspond to the actual base-space sequence, it's only a representation of the color-space sequence. I guess it would be possible to use this trick to make BioStrings and ShortRead work with SOLiD data. However, one very important feature of the SOLiD system, is that the reverse complement sequence corresponds to the reverse color-space sequence (there is no "complement" in color-space). This means that the algorithm for returning the rev-comp sequence when prior to matching on the (-)-strand need to be re-written to report the reverse sequence instead of the rev-comp. Did all this make sense...? Basically, I think it would be possible to make it work if the colors are "double-encoded" and the internal function that rev-comps a sequence is modified to report the reverse. Best Daniel Klevebring On 5 feb 2009, at 01.39, Martin Morgan wrote: > , once reads are represented > as traditional nucleotide sequences (which I guess they must be at > some point?). -- Contact information: Daniel Klevebring M. Sc. Eng., Ph.D. Student Dept of Gene Technology Royal Institute of Technology, KTH SE-106 91 Stockholm, Sweden Visiting address: Roslagstullsbacken 21, B3 Delivery address: Roslagsvägen 30B, 104 06, Stockholm Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075, SE-10450 Stockholm E-mail: [email protected] E-mail: [email protected] Phone: +46 8 5537 8337 (Office) Phone: +46 704 71 65 91 (Mobile) Web: http://www.biotech.kth.se/genetech/index.html Web: http://www.arrayadvice.se/ Fax: +46 8 5537 8481 MSN messenger: [email protected] [[alternative HTML version deleted]]
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