I have some fastq files produced by NextSeq. The average fragment length is between 350-400bp. The library prep adds 139bp of adapters, so the inserts are 200-250bp.
Would the kallisto command look like this?
kallisto quant -i index -o output --single -l 350 -s 50 R1.fastq.gz --rf-stranded
my hunch is that the fragment length only matters when the run is in paired-end mode - in single-end mode I don't see how that would have any effect whatsoever
The kallisto manual says that you need to specify both -l and -s for single end mode. I am just not sure if the values I chose are correct.