how to map a sanger reads to a reference sequence?

[anyone1985]

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?

[bio-x]

you can try new version consed, it can mapping sanger and solexa reads.

good luck

[anyone1985]

Yes, I have tried. However, I do not satisfied with the results. I'd like to know some beter way to mapping the reads.

[Torst]

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?

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/

I have used it for Solexa, SOLID3, Sanger and 454 data with success.

[anyone1985]

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.

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/

I have used it for Solexa, SOLID3, Sanger and 454 data with success.

[BaCh]

Yes, I have tried. However, I do not satisfied with the results. I'd like to know some beter way to mapping the reads.

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.html

B.

Disclaimer: I may be biased, I wrote MIRA.