sleuth differential expression without bootstrap

I was trying to run sleuth for differential expression analysis. But I don't have the kallisto bootstrap values. I am wondering if it can run without bootstrap estimates.

rna-seq

• 2,898 views • link

written 8.9 years ago by Pappu

If you have no bootstraps I'm pretty sure you can't prep the quantification for Sleuth. I had this issue when trying to run Salmon converted estimates (no bootstraps) in Sleuth and it threw an error.

• 0 views • link

written 8.9 years ago by andrew.j.skelton73

0 answers

No answers yet.

More posts like this

kallisto normalized TPM values without bootstraps
written 2.9 years ago by butterman16 •

Hi everyone! I have quantified the RNA expression in a large number of samples using kallisto, however, I did not include any bootstrapping in my …
Salmon: Any downstream DEA tools which uses abundance estimate variation information?
written 7.5 years ago by Thomas

Dear Biostars community, I was just wondering if there are any differential expression analysis tools which can be used downstream of `Salmon`, which incorporates abundance …
combining reads from multiple lanes for DE analysis
written 7.5 years ago by Pappu

I am tying to do differential expression (DE) analysis between different conditions. Now I have same samples sequenced at multiple lanes to improve coverage. I …
Is Kallisto Sleuth pipeline suitable for all organisms?
written 8.2 years ago by SMILE

Hi all, I prefer to use Kallisto-Sleuth pipeline to do differential gene expression analysis now. But there is one thing I am not sure, is …
Utility of Kallisto bootstraps when not using sleuth downstream
written 8.5 years ago by kautilya

Does the bootstrap option for kallisto have any utility if sleuth is not going to be used downstream? In a small test I did the …
Data Visualization Web App
written 8.6 years ago by Pappu

I am trying to make a data visualization web app in Python where users can visualize their gene expression mutation etc data sets and run …
Does Anyone understand the Sleuth Shiny app used to visualize your RNA-seq Data??
written 8.6 years ago by williamsbrian5064

I was wondering if anyone knew how to interpret the Sleuth RNA-seq data? The column names are "pval", "qval", "rss", "sigma_sq", "tech_var", "mean_obs", "var_obs", "sigma_sq_pmax", …
Sleuth_fit error "`Error in if (sum(valid) == 0) { : missing value where TRUE/FALSE needed"
written 8.7 years ago by williamsbrian5064

Hi, I am using Sleuth to generate some RNA-seq data. I keep getting this error when I try to run the program and I was …
get gene ids running sleuth kallisto for differential gene expression
written 10.4 years ago by frida.danielsson •

Hi, I'm trying to run sleuth to look for differential gene expression between two conditions, but I find the manual a bit hard to interpret. …
Visualize Raxml 8 Bootstrap Tree
written 12.5 years ago by Pappu

I am trying to visualize the tree using ete2 and figtree. But the programs don't seem to understand the bootstrap value given in `RAxML_bipartitionsBranchLabels.test` as …