Setting Unicycler parameters for workflow.

[ambarishK]

Sir, I am forming workflow using Unicycler. I have to set two parameters --min_fasta_length and
--linear_seqs as 10000 and 1 respectively. I have set it while workflow formation and save it to use both the parameters for the next time. Each time it ask to set the parameters at run time rather using them as hardcoded values.

[wm75]

Are you still facing this issue, or did you manage to resolve it?

[ambarishK]

Sir. each time while running the workflow I have to set both ones. What I wanted to fix or hard-code at the time of workflow formation. But it does not happens so.

Running it after setting both parameters at run time.

[ambarishK]

One more error related DESeq2 is there. I am trying to get differential expression of genes across four SRR accessions. Lets say SRR1*****, SRR2*****, SRR3***** and SRR4*****.

But DESeq2 asks for replicates. I am passing on each SRR* feature count matrix as separate sample ( factor level ) but it does not work.

I am posting the error below.

estimating size factors
estimating dispersions
Error in checkForExperimentalReplicates(object, modelMatrix) : 

  The design matrix has the same number of samples and coefficients to fit,
  so estimation of dispersion is not possible. Treating samples
  as replicates was deprecated in v1.20 and no longer supported since v1.22.

Calls: DESeq ... estimateDispersions -> .local -> checkForExperimentalReplicates

This is my shared history

https://usegalaxy.eu/u/ambarishk/h/de-novo

Please resolve the DESeq2 error on priority.

[wm75]

So DESeq2 first: thing is it requires replicates as you found out already. If you don't have those, you cannot use DESeq2. Probably the best you could do is calculate some general descriptive stats across samples and genes and to look for clear outliers, i.e. do some exploratory analysis in an ipython notebook.

[wm75]

For the strange workflow parameter error:

• which browser are you doing this in (there maybe some subtle issues similar to what you are seeing with Microsoft browsers - both IE and Edge). Recommended browsers are Chrome/Chromium and Firefox. Safari and other webkit-based browsers should also work in general.
• when you save a workflow with those parameters configured correctly and you leave the workflow editor and go back into it, do you see those settings preserved?

[ambarishK]

I am using Crome. I saved the workflow with both the parameters. It works now.

Thank you so much.

For DESeq2, how to do analysis in ipython notebook?