Question: How to run sleuth in single run mode?
0
gravatar for aquaq
14 days ago by
aquaq10
aquaq10 wrote:

Hi!

I have run kallisto on RNA-Seq data from SRA. Unfortunately, it does not have any replicates. After kallisto, I try to run sleuth with recommended commands (https://pachterlab.github.io/sleuth_walkthroughs/trapnell/analysis.html). However, sleuth_fit gives an error the exact same as described in this thread: https://groups.google.com/forum/#!topic/kallisto-sleuth-users/nLtzFHqUm2Y Towards the end of the thread, somebody mentions that single run mode have been implemented and should be soon available (as at 11/2017). I still cannot find any mention of it in the tutorial, description, etc. Does anybody know whether it has been released and how to run sleuth in this mode properly?

I appreaciate all help!

rna-seq kallisto sleuth • 75 views
ADD COMMENTlink written 14 days ago by aquaq10

The way I understand that thread, sleuth_live, not sleuth now has a single library running mode - sleuth_live is the web server for explanatory data analysis, it doesn't do differential expression

ADD REPLYlink written 14 days ago by Philipp Bayer5.7k

You are right, I have misread it. Thank you!

ADD REPLYlink written 14 days ago by aquaq10
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