Hi, I'm trying to correct 454 homopolymer errors with solexa reads. Because we can't directly take the mira assembly as such as a backbone (there are some contig joining to do), we extracted the assembled consensus, mapped the 454 reads to it, and in a second time, mapped the solexa reads (36bp) to it. I'm now going through all SROc and/or STMS tags, just to check the results. It works fine for most of the cases, but I had several cases where there are 5-10 solexa reads whose last or first base is not well aligned (there is a gap in the rest of the reads), and the consensus is changed by those 5-10 reads. I've attached two screenshots from my consed window. The consensus should clearly be * (there are ~100 reads that say so), but the 7-8 solexa reads impose a A in the consensus. The STMS tag reads (somewhat elusively): Solved vote: / sxa (1) A 41 is in Seems like a strange border effect... Cheers, Lionel
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