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Hi all,
I am currently working on analyzing amplicon reads from a 454 sequencer. One of the things I want to do is realign my reads around known indels. I know that full indel realignment of 454 data is a problem (per http://www.broadinstitute.org/gsa/wi..._around_indels), but it's unclear to me whether or not known-only realignment is a good idea.
Do any of you have experience with this? I'd appreciate advice.
alex
I am currently working on analyzing amplicon reads from a 454 sequencer. One of the things I want to do is realign my reads around known indels. I know that full indel realignment of 454 data is a problem (per http://www.broadinstitute.org/gsa/wi..._around_indels), but it's unclear to me whether or not known-only realignment is a good idea.
Do any of you have experience with this? I'd appreciate advice.
alex