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Old 11-21-2011, 06:50 AM   #3
poorphd
Junior Member
 
Location: lawrence,ks 66046

Join Date: Jul 2011
Posts: 3
Default no, not that simple

In classical biology, we define "Forward" is the direction from 5' to 3' and "Reverse". 3' to 5'. but in NGS sequencing, all the sequences direction is from 5' to 3' , so F means sense strand, and R means anti sense.but in classical biology, we define sense strand is mRNA direction. those concepts are a little confusing.

and also in the Trinity algorithm, i think sense or antisense is just oppossite to each other. if you define one srtand is sense, the other one is antisense. trinity donot care which one is which one. i think you design this parameter --SS_lib_type, just to make the output sequences following
the sense direction which defined by users.
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