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Old 06-27-2011, 09:46 AM   #1
AnamikaDarwin
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Question Evidence of Strand Bias

Hello,


For my SNP positions, I am getting count of reads that are each on the forward and reverse strands. If there were no strand bias one expects the ratio of these counts to be centered around 1.

Any recommendations of a threshold value, above which it can be inferred as evidence of strand bias? Or is this approach to na´ve?

Thanks,
Mika
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Old 06-27-2011, 05:21 PM   #2
nilshomer
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Quote:
Originally Posted by AnamikaDarwin View Post
Hello,


For my SNP positions, I am getting count of reads that are each on the forward and reverse strands. If there were no strand bias one expects the ratio of these counts to be centered around 1.

Any recommendations of a threshold value, above which it can be inferred as evidence of strand bias? Or is this approach to na´ve?

Thanks,
Mika
See the strand bias p-value with "samtools mpileup -S". This would give a good statistical interpretation of such a bias.
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