kallisto -s 0 error

[한지헌]

Hello, I am a student who is trying to do deg through kallisto. The fastq data I use is single end, all sequences are 100bp, and sd is 0. I used kallisto quant -i index -o output --single -l 100 -s 0 fastq and an error occurs. Is there a way to solve this problem? Thank you.

[Pall Melsted]

-l and -s refer to the library size, i.e. the fragments sequenced, not the read size. If you have measurements from a bioanalyzer machine indicating a distribution of the fragment size you can use those numbers. Otherwise I would recommend sensible defaults e.g. -l 200 and -s 50, depending on how the size selection was done

On Thu, Mar 9, 2023 at 11:47 AM 한지헌 <jiheonh...@gmail.com> wrote:

Hello, I am a student who is trying to do deg through kallisto. The fastq data I use is single end, all sequences are 100bp, and sd is 0. I used kallisto quant -i index -o output --single -l 100 -s 0 fastq and an error occurs. Is there a way to solve this problem? Thank you.

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