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Old 04-28-2014, 10:53 AM   #1
Turner Conrad
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Default Strange strand bias and unusual depths

Hi all,

I'm seeing some very strange stuff with a resequenced prokaryotic genome coming from an Illumina HiSeq 2000. The design is 50bp single end and workflow is BWA-mem, GATK indel realignment, and visualization with the MATLAB NGS browser. There is a complete negative strand bias with a small island of positive strand bias, an 6pb segment of depth that is 5x normal for the rest of the genome (2300- vs 480-fold), nearly completely mapq 0, and distinct breakpoints. See the attached figure for a visualization.

Any ideas what kind of phenomenon could be causing this?
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Old 04-28-2014, 11:10 AM   #2
Brian Bushnell
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Probably incorrect alignment around a structural variation. But, I'm used to IGV so I don't quite understand the picture.
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Old 04-28-2014, 04:32 PM   #3
Turner Conrad
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Well, it's centered around a duplicate rDNA region, but is there anything about BWA that would introduce such a strong strand bias when trying to pick which copy to map to?
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Old 04-28-2014, 05:26 PM   #4
Brian Bushnell
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Not that I've noticed. Be sure you're using the latest version. Also, try a different aligner like BBMap or Bowtie2 to see if you get the same results. If you do, it's not an algorithmic problem, but something in the data.
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coverage, depth, duplication, repeat, strand bias

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