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Old 11-09-2008, 02:12 PM   #4
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Location: Sweden

Join Date: Mar 2008
Posts: 324

what advantage do you see with SHRiMP compared to the ABI tools? It is said to be very slow?

Direct conversion is not possible for reads that have any sequencing error since it will change all following bases in base space. Your coversion look correct though, but it is very common that sequences have at least one cs error. SOCS and ZOOM! are supposed to do colorspace alignments, perhaps worth a try.
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