I have about 3300 reads from foxmid library and I'd like to maping to a reference sequence, how should I do? I also have some solexa data to improve my sequence quality. Can I use the some software to map or different?
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you can try new version consed, it can mapping sanger and solexa reads.
good luck -
Yes, I have tried. However, I do not satisfied with the results. I'd like to know some beter way to mapping the reads.Comment
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SHRiMP will happily align both your Solexa and Sanger reads to your reference sequence, allowing for both indels and substitutions: http://compbio.cs.toronto.edu/shrimp/Originally posted by anyone1985 View Post
I have used it for Solexa, SOLID3, Sanger and 454 data with success.Comment
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Thank you for your answer. Can the SHRiMP output the result in the format of ace? I would like to calculate the sequence quality, too.
Originally posted by Torst View PostComment
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You might want to try MIRA, it'll happily map Sanger, 454 and Solexas for you and shell out the results as FASTA, CAF, ACE ... . Screenshot of 454 and Sanger reads mapped to a reference: http://chevreux.org/mira_ex_454sanger.htmlOriginally posted by anyone1985 View Post
B.
Disclaimer: I may be biased, I wrote MIRA.Comment
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