Now I have my first Solexa data, as it's for MT, which is circular, therefore, some of the reads will overlap the begining and ending, is there some software that can do local alignment, which means, part of the read aligns to the begining and other aligns to the ending?
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I use the following for mt when aligning against the human NCBI ref and it seems to do the job.
1234678:PAIR_PARAMS --circular=cMT.fa --min-single-read-alignment-score=1
If you don't have paired end you could probably do something a bit brute force and create two genome files, one normal and one with the beginning offset a few hundred base pairs (cut a bit of the end and move it to the beginning). Then a quick script should be able to correct and combine the two. Or you could use a different aligner than eland.
BradLast edited by basickler; 04-17-2009, 08:02 AM.
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I don't do wet work. What I can tell you is they tried lots of primers, and most of them don't work, even works, only on some individuals.
concerning the barcoding, we use the protocol published on nature protocol 2008 which is for 454, meanwhile, we are designing new protocol.
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