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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

Will that do the trick?

shayeste 03-10-2014 11:35 PM

hello everyone
I am a new member

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