RNA seq Adapter calculation

Question

[thekid2018]

Hello,

I have been analyzing RNA-Seq data and recently was requested to provide Adapter metrics. I am not sure if there are any tools out there that can determine the Adapter metrics. And also how this metrics is calculated. I normally trim the adapter sequence before the analysis.

Any help in identifying how this is calculated is appreciated. Google searches using various combinations returned nothing, except for one instance where : Adapter <.03, From RNA-SeQC v1.1.9 stats was mentioned in a xls document.

I have gone through RNA-SeQC v1.1.9 but do not see the metric.

Thank you, thekid

[h.mon]

I suppose adapter metrics is just the number and percentage of reads containing adapters, and the number and percentage of bases removed. Do you want more information than that?

I know bbduk output these stats, and some more if you use the parameter stats=file.txt. I beieve Trimmomatic (and probably other programs) also outputs similar metrics.

[thekid2018]

Hello,

Thank you for that information. So I am guessing that the adapter metrics looks let the number of reads that have adapters even after trimming?

So would it be possible to call the adapter metrics that is calculated as contamination of the reads with adapters after trimming?

Would the RNA-SeQC do the same, curious about this since I found this on a NIH website??

Thank you, thekid

[h.mon]

When one trims adapters, the intention is to remove all of them, because they are noise, not signal. If the adapter was not removed, it is because the software didn't recognize it - so the same software which removed adapters can't quantify left-over adapters. So I guess adapter metrics refer to adapter contamination before adapter removal, not after.