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Old 10-29-2013, 10:40 AM   #1
crayfish
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Location: usa

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Default Call SNP

Hi,everyone, I have two samples (A and B) they are the same species with different phenotype, I got 454 transcriptome data for both of them, I want to detect the SNP between A and B, means I want to find some SNPs that can distinguish A and B, I do not have reference genome, so I use the de novo transcriptome assemble as reference. so can you suggest some software that i can use?

thank you
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Old 10-29-2013, 11:28 AM   #2
nucleus
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Take a look at Cortex (http://cortexassembler.sourceforge.n...ortex_var.html), I think it can be used without a reference,
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Old 10-29-2013, 11:43 AM   #3
crayfish
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Thank you, i will try it
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