Question: Differentially expressed genes with sleuth- RStudio
0
gravatar for amina.alhalwany
18 months ago by
amina.alhalwany0 wrote:

Hello I need a help in analyzing deferentially expressed genes with I have a Kallisto data with 6 folders for RNA seq. and an identification file for info. as the following:

run_accession   experiment_accession    Index   condition   sample

pC1-a   pC1-6a  Rip-GFP/Col-a   control Xiao-Ning
pC2-b   pC1-6b  Rip-GFP/Col-b   control Xiao-Ning
pC3-c   pC1-6c  Rip-GFP/Col-c   control Xiao-Ning
p9-1    p9-1-6g Rip-OX9-1   p9  Xiao-Ning
p9-2    p9-2-6h Rip-OX9-2   p9  Xiao-Ning
p9-3    p9-3-6j Rip-OX9-3   p9  Xiao-Ning

and my task is analyzing them with the sleuth on R studio I have a certain script as the following:

source("http://bioconductor.org/biocLite.R")
biocLite("rhdf5")
biocLite("biomaRt")

biocLite("devtools") # only if devtools not yet installed
install.packages('devtools')
devtools::install_github('pachterlab/sleuth')
install.packages('shiny')

library("sleuth")

base_dir <- "C:/Users/asus/Desktop/data"

sample_id <- dir(file.path(base_dir,"results"))

kal_dirs <- sapply(sample_id, function(id) file.path(base_dir, "results", id, "kallisto"))

s2c <- read.table(file.path(base_dir, "hiseq_info_rip_p9.txt" ), header = TRUE, stringsAsFactors=FALSE)
s2c <- dplyr::select(s2c, sample = run_accession, condition)
s2c
s2c <- dplyr::mutate(s2c, path = kal_dirs)
print(s2c)
so <- sleuth_prep(s2c, ~ condition)
so <- sleuth_fit(so)
so <- sleuth_wt(so, 'conditionp1')
models(so)
sleuth_live(so)
results_table <- sleuth_results(so, 'conditionp9')

and the script is working but I am facing a problem as the following:

reading in kallisto results
......
Error in check_kal_pack(kal_list) :
Inconsistent number of transcripts. Please make sure you used the same index everywhere.

so <- sleuth_fit(so)
Error in is(obj, "sleuth") : object 'so' not found
so <- sleuth_wt(so, 'control    Xiao-Ning')
Error in is(obj, "sleuth") : object 'so' not found
models(so)
Error in models(so) : object 'so' not found
sleuth_live(so)
Error in is(obj, "sleuth") : object 'so' not found
results_table <- sleuth_results(so, 'Xiao-Ning')
Error in is(obj, "sleuth") : object 'so' not found

I would appreciate any small details that could help, thank you!

genome rna-seq sequence R gene • 1.1k views
ADD COMMENTlink modified 17 months ago by Biostar ♦♦ 20 • written 18 months ago by amina.alhalwany0

The key is "Inconsistent number of transcripts", which suggests that you quantified against different things. Fix that.

ADD REPLYlink written 18 months ago by Devon Ryan85k

can you help me fixing it ?

ADD REPLYlink written 18 months ago by amina.alhalwany0
1

Just run kallisto against the same reference transcriptome for every sample. If you already did that, you probably have some truncated file.

ADD REPLYlink written 18 months ago by h.mon20k
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