In RNA-seq, paired ends, stranded, done with TrueSeq - what parameter in tophat should be applied to see strandedness properly?
fr-firststrand or fr-secondstrand ?
I am a bit confused, seen also the hints on reverse complement or swapping the order of R1 and R2 in the command line. (http://www.biostars.org/p/64250/)
Thanks for the hints!
fr-firststrand or fr-secondstrand ?
I am a bit confused, seen also the hints on reverse complement or swapping the order of R1 and R2 in the command line. (http://www.biostars.org/p/64250/)
Thanks for the hints!
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