Question: Bioanalyzer: fragment length and standard deviation for kallisto
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gravatar for piero
2.9 years ago by
piero20
piero20 wrote:

Hi there,

I have obtained mRNA-seq data for several samples on a HiSeq 4000 system, SE, TruSeq Stranded protocol. I want to use kallisto to process my data, and on the manual it is stated that for SE I would need to specify the fragment length and its standard deviation, which I could get from the library prep QC on the Bioanalyzer. So if I look at the QC of one of my samples (HERE) , I guess the average fragments length of that sample is 291 bp (Adapted Dimer 0.2%), right? What about the standard deviation? Where do I get this value? Shall I just try to 'visually' extrapolate it from the peak? So ~~25?

rna-seq • 1.8k views
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