How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
I have RNA-seq read quantification results from Kallisto. Kallisto has output 1) estimated counts, and 2) tpm values. I am hoping to perform DESEQ2 analysis on these data. The DESQ2 documentation suggests that I should be using only count data as input. However, both of the Kallisto outputs are not discrete counts. They are continuous real numbers. What is the proper preprocessing to use Kallisto quantification tables on DESEQ2?
2 answers
just round it up!
Log in to answer this question.
More posts like this
-
getting RNA-seq raw counts from Kallisto
written by Meghan.T •
-
What purposes can TPM values be used for?
written by JH •
-
Segway - Using continuous and discrete tracks
written by corinsexton •
-
Kallisto: Estimated average fragment length
written by jayeshkumarsundaram •
-
How is the bootstrapping information from kallisto treated in DeSeq2 when imported using tximport?
written by divya.nandakumar •
-
Real-valued HTseq count to DESeq2
written by english.server
-
Performing differential expression study on isoforms
written by glady
-
How to convert transcript level TPM to gene level TPM ?
written by k.kathirvel93
-
Using bootstrap testing in kallisto to obtain estimated transcript counts
written by neuner.sarah •
-
Confusion in HTSeq paired-end output count
written by Whoknows
