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alyssafrazee / polyester

Bioconductor package "polyester", devel version. RNA-seq read simulator.
http://biorxiv.org/content/early/2014/12/12/006015
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Update polyester.Rmd #19

Closed mikelove closed 9 years ago

mikelove commented 9 years ago

did you mean (transcript length - read length) here for the effective length?

jtleek commented 9 years ago

Are we sure it is supposed to be minus? I thought the deal here was you were taking the transcript length, dividing it by read length, and mulitplying by 20 to get average coverage across samples.

alyssafrazee commented 9 years ago

Exactly what @jtleek said -- it should be dividing the transcript length by the read length (which would give you the number of reads you'd need for ~1x coverage), then multiplying by the coverage factor.

mikelove commented 9 years ago

thanks for the quick explanation. I was thinking, "want 20 reads starting from each position in the tx"

but you do say coverage and i get it now