Deleted and reposted this to ask an actually sensible question. Sorry to those who've had to see an iteration of this twice.
I am intending to use Kallisto and was looking for an opinion re: estimating fragment length. We used a Lexogen 3’ QuantSeq kit. Here is a sample Bioanalyzer trace of one of the library preps.
Using kallisto for 3' QuantSeq was discussed in this paper, using l=100 s=30 to run kallisto quant. Looking at the GEO page for the prior study the authors accessed, however, I did not see these values listed (was this an approximation for convenience?).
Should I use the smear analysis (in red) or use the data called for peak 2, the 258 bp peak? The smear analysis boundaries were set manually at our sequencing core and the peak calling was automated. I am a little more inclined to go with the automated peak calling, however, I wanted to verify. Or should I use the approximation in the publication, which gave useful results?