Kallisto estimated sd and fragment length
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3.1 years ago
bharata1803 ▴ 530

Hello,

I want to ask about the significance of sd and fragment length for Kallisto. Will Kallisto prduce totally different result if the parameter is different? I use from public data and it mention like this: "RNA-seq was performed using Illumina HiSeq 2500 System with 100 nucleotide single-end reads. One sample and its paired non-tumoral tissue were eliminated from the subsequent analysis because of bad RNa quality."

So, I think the value for frament should be 100 but I don't know the sd value. I just use 30 because in another post mentioned that sd 30 is normal for RNA-seq (although it was also mentioned that fragment 200 is typical).

So, is it a good parameter? I check the TPM between Kallisto and Salmon and it somehow different. Kallisto produce a bit higher TPM compare to Salmon result.

RNA-Seq kallisto alignment • 1.6k views
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