Question: Using Kallisto and Sleuth for RNA-seq analysis - do I have to normalise before differential analysis?
gravatar for a.rex
14 months ago by
a.rex110 wrote:

I am relatively new to RNA-seq analysis, and I have been using Kallisto and Sleuth for this.

My code looks like this - I run an LRT test first on the data, and then a Wald's test on those that have passed this filter. I end up with a list of loci that are differentially expressed between my two condition ('kd' versus 'control').

base_dir <- "/path/to/data"
samples <- paste0("sample",1:4)
kal_dirs <- sapply(samples, function(id) file.path(base_dir, id))
s2c <- read.table(file.path(base_dir, "kd.txt"), header = TRUE, stringsAsFactors=FALSE)
s2c <- dplyr::select(s2c, sample = sample, condition)
s2c <- dplyr::mutate(s2c, path = kal_dirs)
so <- sleuth_prep(s2c, ~condition)
so <- sleuth_fit(so)
so <- sleuth_fit(so, ~1, "reduced")
so <- sleuth_lrt(so, 'reduced', 'full')
so <- sleuth_wt(so, ‘conditionkd’)
results_wt <- sleuth_results(so, 'conditionkd')
results_lrt <- sleuth_results(so, 'reduced:full', test_type = 'lrt')
kd.lrt.sig_ids <- results_lrt$target_id[which(results_lrt$qval < 0.05)]
kd.wt.sig_ids <- results_wt$target_id[which(results_wt$qval < 0.05)]
kd_ids <- kd.wt.sig_ids[kd.wt.sig_ids %in% kd.lrt.sig_ids]
shared_results <- results_table_wt[results_table_wt$target_id %in% shared_ids,]
write.csv(shared_results, file=“/path/to/kallisto_wald_test_lrt_passed_kdd3.csv")

However, do I have to first normalise the TPM/count column on the abundance.tsv file produced Kallisto for each of the samples? Or is this incorporated in the tests? No online tutorials have done this, so how is it normalising libraries?

rna-seq • 1.2k views
ADD COMMENTlink written 14 months ago by a.rex110

Hope this could be helpful:

so <- sleuth_prep(s2c, ~ condition)
## reading in kallisto results
## ......
## normalizing est_counts
## 50844 targets passed the filter
## normalizing tpm
## merging in metadata
## normalizing bootstrap samples
## summarizing bootstraps
ADD REPLYlink modified 14 months ago • written 14 months ago by bioinfo890
gravatar for a.rex
14 months ago by
a.rex110 wrote:

Sorry I realised that this is a silly question - so <- sleuth_prep(s2c, ~condition) does the tpm normalisation between samples

ADD COMMENTlink written 14 months ago by a.rex110
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