Mapping ratio when alignment 37bp human NGS reads to mouse genome
Hi Sequencers:
Is there any empirical intuition what's the appropriate proportion of the reads when we map 37bp human reads to mouse genome?
Best regards
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Ram
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Shicheng Guo
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Shicheng Guo
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No, it depends on a huge number of factors such as the data quality, contamination rate, preprocessing steps, mapping software and parameters, etc. If all of those are good, ~98% is not unreasonable.