Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Cufflink Error (Galaxy)
0
gravatar for howard_saw
3.8 years ago by
howard_saw • 10
United Kingdom
howard_saw • 10 wrote:

Hi,

I've done Tophat with my sequencing reads and I'm trying to do Cufflinks. However, i keep getting this error sequence,

"cufflinks v2.1.1
cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -N -b ref.fa
Error running cufflinks.
return code = 1
Command line:
cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -N -b ref.fa /galaxy-repl/mai"

AND "Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values."

Does anyone know what is going on? At first I thought it might be my Reference sequence, but then the reads was mapped successfully using that sequence in the Tophat step.

Does anyone know how to solve the problem?

Thank you.

Best wishes

Howard
rna-seq galaxy cufflinks • 917 views
ADD COMMENT • link •
modified 3.8 years ago by Martin Čech ♦♦ 4.9k • written 3.8 years ago by howard_saw • 10
0
gravatar for Martin Čech
3.8 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

Did you try to use the 'auto-detect' for metadata? (Click the pencil button on the dataset and then 'Auto-detect' button.)
ADD COMMENT • link written 3.8 years ago by Martin Čech ♦♦ 4.9k

Hi Martin,

I did, but it still failed. Do you know what is the reason?

Thank you.
Howard

ADD REPLY • link written 3.8 years ago by howard_saw • 10

Are you working on the https://usegalaxy.org server?

ADD REPLY • link written 3.8 years ago by Martin Čech ♦♦ 4.9k

Hi Martin, 

Yes I am, is it something wrong with my dataset?

Thank you.

ADD REPLY • link written 3.8 years ago by howard_saw • 10
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: 181 users visited in the last hour