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-   -   Find SNP in Sanger sequenced gene (http://seqanswers.com/forums/showthread.php?t=9157)

genelab 01-30-2011 09:41 PM

Find SNP in Sanger sequenced gene
 
Hi guys,
I have about 120 sequences of the same genes from our sample, which are sequenced by Sanger methods, How can I get the SNP sites among this gene compared to the reference gene? Is there any software can help me do this?

Any sugestion will be highly appreciated!

dagarfield 01-31-2011 01:39 PM

My recommendation would be to align the reads to your reference using the long read option in BWA or Lastz (or something else with long read capacity) and output a SAM file. You should be able to get SNPs out of the SAM file pretty easily following the SAM Tools FAQ here
http://sourceforge.net/apps/mediawik...?title=SAM_FAQ

Will that do the trick?

shayeste 03-10-2014 11:35 PM

hello everyone
I am a new member


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