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imgag / ngs-bits

Short-read sequencing tools
MIT License
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Trimmed base percentage not correct for long read alignments #468

Open jakobmatthes opened 1 year ago

jakobmatthes commented 1 year ago

Calculation of trimmed base percentage assumes that all (most) alignments have the same length. For long read data, this is not valid. Reported trimmed base percentages are very high.

https://github.com/imgag/ngs-bits/blob/9e19e7ac7130220abb4adc9c241cccdfe4fbc89f/src/cppNGS/Statistics.cpp#L904

https://github.com/imgag/ngs-bits/blob/9e19e7ac7130220abb4adc9c241cccdfe4fbc89f/src/cppNGS/Statistics.cpp#L996

leonschuetz commented 1 year ago

Does this parameter even make sense for long-read data? Because there is no adapter trimming (so far). Should we simply remove it for long-reads?