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Old 11-17-2010, 03:55 AM   #1
Inti
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Default which alignment tool allows to anchor pair end reads over repeats?

Hi guys,
I'm having a problem using Eland for pair end alignment over repeats since it seem to need both reads to be unique to match the pair.
Is there any option to specify that it should use the information of one unique read to anchor the second read over a repeat element?
or is there any other program that allows this option.
Thanks!
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Old 11-17-2010, 04:59 AM   #2
lh3
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I know maq, bwa, novoalign and stampy do this. Mosaik, gsnap and many others possibly, too.
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Old 11-17-2010, 01:48 PM   #3
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bfast does too. (postprocess: -g).
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