Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Cufflinks/merge/diff tools deprecated
0
gravatar for aaweiner
10 weeks ago by
aaweiner • 0
aaweiner • 0 wrote:

I've been using a HISAT2 -> Cufflinks -> Cuffmerge -> Cuffdiff -> CummeRbund pipeline to analyze some RNA-seq data. I've used many of these tools through Galaxy before but it seems that Cufflinks, Cuffmerge, and Cuffdiff are all listed as "deprecated" and I couldn't find much on this online or in pervious posts. Will this be resolved soon and are they okay to use while listed as deprecated?

Thanks,

Aaron
rna-seq galaxy cufflinks • 307 views
ADD COMMENT • link •
modified 10 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 10 weeks ago by aaweiner • 0
0
gravatar for Jennifer Hillman Jackson
10 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, the tools are now considered deprecated and will not be updated further. There are known issues with Tophat and Cuffdiff. More issues may come up as Galaxy is upgraded and the tools are not. CummeRbund may also be deprecated soon as there is no way to produce the needed input in Galaxy (this is one of the problems with Cuffdiff - the SQLite database for CummeRbund cannot be created -- and jobs will error if that output option is used).

Try using the new tools/methods instead. This tutorial covers the usage: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 10 weeks ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 168 users visited in the last hour