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Old 09-06-2012, 06:13 AM   #1
kingsalex
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Default fundamental strand bias in sequence data

Does anyone else see fundamental strand bias in many mapped read positions. That is, for exome sequencing I see both reference allele and variant allele in one particular stand only, can be either + or - strand, for many cases, as if only one strand has been aligned or sequenced at those positions? I am using casva 1.8 to align and then resulting BAM files processed with samtools (sort and mpileup) and varscan.

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Old 09-07-2012, 12:44 AM   #2
Lluc
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I'm not familiar with exome sequencing, but I would suspect that the strategy used to enrich the sample in exons may have introduced that bias.
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Old 12-12-2013, 07:52 AM   #3
m_two
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In any capture data the regions farthest from the probes tend to have single stranded coverage if the read length is shorter than the insert length.
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