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Old 02-07-2010, 05:30 PM   #1
Location: US

Join Date: Oct 2009
Posts: 10
Default Mosaik Aligner problem with SOLiD sequences

Hi all,
I have installed Mosaik 1.0 on two desktops to map SOLiD colorspace reads. On one desktop, the Aligner never quite worked: it would always choke on some input read or other with a message like:

"ERROR: Unknown combination found when converting to basespace: [T] & [-]"

I traced the first offending read in one of the input datasets, and there was nothing special about it.

On the other desktop, Mosaik Aligner has been working fine, with only a recent issue similar to the Error described above: I tried to use the option where the reference genome has IUPAC ambiguity letters that allow more matches to them (e.g. an R in the reference could match to both an A or G in the read without a penalty).

But the runs don't seem to work, the aligning process returns immediately errors like "Unknown combination found when converting to basespace: [Y] & [G]" (like I described above, always happes with my other installation).

Anyone seen this issue? Ideas how to resolve it?

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