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Old 05-24-2013, 12:39 AM   #1
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Location: Seoul, Rep. of Korea

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Default The ratio of reads whose mate mapped to different chromosome in targeted sequencing

Hello all,

Recently my team sequenced targeted reads of tumor/normal pair, and the ratio of interchromosomal mapped reads looks weird.

Naturally, tumor should have more interchromosomal translocations than normal, so rate can be higher.
But too high level of cross mapping rate could mean that there were some quality control problems in sample prep process.

So I want to use this ratio as one of my QC.
In my case, tumor samples have the range of 5% to 20% cross mapping rate while normals have 0% to 5%.

Could you give me some guidance for this observation?

Thank you.
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targeted resequencing

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