We are currently using MAQ to align our Solexa reads to our reference sequence. Does anyone know if MAQ can also tell me which parts of my reference sequence have no reads aligned to them? If not, can anyone suggest a program that can tell me this info? Thanks!
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Pretty sure MAQ can't, and a quick scan of the man page didn't yield anything.
Have you tried one of the visualization tools? Only one I know off the top of my head is tablet, but unfortunately haven't had a chance to play with it myself:
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Senthil Palanisami
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Originally posted by mlee View PostWe are currently using MAQ to align our Solexa reads to our reference sequence. Does anyone know if MAQ can also tell me which parts of my reference sequence have no reads aligned to them? If not, can anyone suggest a program that can tell me this info? Thanks!
Beware, being a de-novo assembler, it's a lot more memory intensive than other mapping programs when used for mapping only.
Regards,
B.
Disclaimer: I wrote MIRA. It's useful to me but it might not be for you. Feedback appreciated.
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