Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: CuffDiff Replicates - which files do replicates 0, 1, 2 point to?
0
gravatar for daniel.tonge
20 months ago by
daniel.tonge • 10
daniel.tonge • 10 wrote:

Our CuffDiff group tracking file lists the replicates as follows (second column);

Control 1
Control 0
Control 2
Control 3
Control 4
Obese   0
Obese   1
Obese   2
Obese   3
Obese   4
Obese   5

Is there any way to determine conclusively which accepted hits file relates to each replicate number please? For example, we have an outlier and would like to exclude it but there is no clear way of linking replicate 0 to obese person 23 for example
rna-seq replicates cuffdiff • 621 views
ADD COMMENT • link •
modified 20 months ago by Jennifer Hillman Jackson ♦ 25k • written 20 months ago by daniel.tonge • 10
2
gravatar for Jennifer Hillman Jackson
20 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The order for replicate labels is the same as the order for conditions/replicates originally entered on the tool form. The run information is captured on the "View details" page - click on the "i" icon within an output dataset to view this.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 20 months ago by Jennifer Hillman Jackson ♦ 25k
2
gravatar for daniel.tonge
20 months ago by
daniel.tonge • 10
daniel.tonge • 10 wrote:

Many thanks Jen...much appreciated. I also visualised the alignments in IGB to confirm as in this instance, one sample was significantly higher than the rest.

All the best,

D
ADD COMMENT • link written 20 months ago by daniel.tonge • 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: 180 users visited in the last hour