I'm starting to use kallisto to do transcript-level expression quantification. I have some questions:
kallisto infer the strandness of the input data just like
salmon does (
--libType A)? I guess the answer is no.
2) For other hand,
kallisto has the next to options:
--fr-stranded Strand specific reads, first read forward --rf-stranded Strand specific reads, first read reverse
Are these options only working for PE data?
3) Regarding the fragment length estimation when using SE datasets:
-l, --fragment-length=DOUBLE Estimated average fragment length -s, --sd=DOUBLE Estimated standard deviation of fragment length (default: -l, -s values are estimated from paired end data, but are required when using --single)
DOUBLE mean? Do we have to specify the double of the number calculated?
Thank you in advance