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Old 01-30-2011, 10:41 PM   #1
Location: honston

Join Date: Nov 2009
Posts: 27
Default 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!
genelab is offline   Reply With Quote
Old 01-31-2011, 02:39 PM   #2
Location: Heidelberg, Germany

Join Date: Aug 2010
Posts: 39

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?
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Old 03-11-2014, 12:35 AM   #3
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Location: Iran

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hello everyone
I am a new member
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