Question: CuffDiff Replicates - which files do replicates 0, 1, 2 point to?
0
gravatar for daniel.tonge
12 days ago by
daniel.tonge0 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

cuffdiff • 29 views
ADD COMMENTlink modified 12 days ago • written 12 days ago by daniel.tonge0
2
gravatar for Jennifer Hillman Jackson
12 days ago by
United States
Jennifer Hillman Jackson21k 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 COMMENTlink written 12 days ago by Jennifer Hillman Jackson21k
1
gravatar for daniel.tonge
12 days ago by
daniel.tonge0 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 COMMENTlink written 12 days ago by daniel.tonge0
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