Hello,
I am having trouble understanding a point made in the Diginorm paper:
http://arxiv.org/pdf/1203.4802v2.pdf
They say that Diginorm discards some terminal kmer and low-abundance isoform information but I am wondering why this is?
According to the description of the algorithm, Diginorm estimates read coverage by using the median abundance of kmers for each read and discards the read if the median abundance is above some cutoff level. This should mean that any low abundance reads would be retained. If this is true, under what situations would it discard reads pertaining to terminal kmers and low-abundance isoforms?
I suspect I am missing something here and it would be very helpful to get some outside views to get me out of this mind trap.
Thank you!
I am having trouble understanding a point made in the Diginorm paper:
http://arxiv.org/pdf/1203.4802v2.pdf
They say that Diginorm discards some terminal kmer and low-abundance isoform information but I am wondering why this is?
According to the description of the algorithm, Diginorm estimates read coverage by using the median abundance of kmers for each read and discards the read if the median abundance is above some cutoff level. This should mean that any low abundance reads would be retained. If this is true, under what situations would it discard reads pertaining to terminal kmers and low-abundance isoforms?
I suspect I am missing something here and it would be very helpful to get some outside views to get me out of this mind trap.
Thank you!
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