Question: How to run sleuth in single run mode?
0
gravatar for aquaq
23 months ago by
aquaq30
aquaq30 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 • 716 views
ADD COMMENTlink written 23 months ago by aquaq30

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 23 months ago by Philipp Bayer6.8k

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

ADD REPLYlink written 23 months ago by aquaq30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 949 users visited in the last hour