Originally posted by kmcarr
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Originally posted by cement_head View PostNope - You've misinterpreted the paper. It doesn't actually say that - it says that using the USS alone is problematic - but the combination of USS and STL is not.
Second, they failed to present any data demonstrating significant levels of PCR duplication in the data in the first place. What is needed in Fig. 5 is a curve plotting number of reads mapped for each of the 24 ERCC controls or mRNAs with out first doing any de-duplication by either USS alone or USS+STL. Only if that curve was significantly higher than the USS+STL curve (blue line in Fig. 5) could they make for adding molecular indexes to RNA-Seq libraries.
What the white paper is attempting to do is to sell a solution without first demonstrating a problem which needs solving.
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Originally posted by kmcarr View PostI stand by my statements. USS would be problematic if duplicate removal was standard practice for RNA-Seq data. It is not.
Second, they failed to present any data demonstrating significant levels of PCR duplication in the data in the first place. What is needed in Fig. 5 is a curve plotting number of reads mapped for each of the 24 ERCC controls or mRNAs with out first doing any de-duplication by either USS alone or USS+STL. Only if that curve was significantly higher than the USS+STL curve (blue line in Fig. 5) could they make for adding molecular indexes to RNA-Seq libraries.
What the white paper is attempting to do is to sell a solution without first demonstrating a problem which needs solving.
Here is a link to example data that demonstrates the difference between USS usage and USS + STLs usage: http://www.biooscientific.com/Portal...lar-Labels.pdf
I hope this clears up your queries.
Regards,
Andor
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