Question: Error in running the RNA-Seq workflow

4.0 years ago by

United States

karanbir • 0 wrote:

I am trying to run workflow on one set of samples (RNA-Seq experiment. But after entering all the information regarding samples and parameters for different modules (TopHat, Cufflinks, etc) when i press on "Run the workflow". it gives the following error:

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Let me know if you need to see the workflow itself (i can send you that too)

Kindly let me know what could be the problem? I would highly appreciate if you could let me know about this at the earliest as i have to finish up some work before the Monday deadline (i.e.11/24/2014)

thanking you,

Karan

rna-seq • 992 views

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modified 4.0 years ago • written 4.0 years ago by karanbir • 0

4.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Please re-run the workflow this morning, if you have not already. Let us know if you continue to have problems.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 4.0 years ago by Jennifer Hillman Jackson ♦ 25k

It still gives the same error :(

As my workflow involves RNA-Seq analysis using 64 steps (different tools which might require high memory?)

Can i use some more resources to run my workflow (maybe high performance computer server?).If so, do you know how could i do that?

thanks

ADD REPLY • link written 4.0 years ago by karanbir • 0

4.0 years ago by

karanbir • 0

United States

karanbir • 0 wrote:

It still gives the same error :(

As my workflow involves RNA-Seq analysis using 64 steps (different tools which might require high memory?)

Can i use some more resources to run my workflow (maybe high performance computer server?).If so, do you know how could i do that?

thanks

ADD COMMENT • link written 4.0 years ago by karanbir • 0

4.0 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

Sorry for the potential misinformation in the error message. This doesn't have anything to do with the resource requirements of your workflow -- the error I'm seeing on the back end is that we "Failed to match up multi-select inputs, must select equal number of data files in each.".

How exactly are you selecting and running multiple samples?

ADD COMMENT • link written 4.0 years ago by Dannon Baker ♦ 3.7k

4.0 years ago by

karanbir • 0

United States

karanbir • 0 wrote:

Thanks for replying back.

Yes for each experiment i have 3 biological reps. For each replicate, i have different number of paired reads from RNA-Seq data (which i select individually/replicate) e.g.

Sample C8 (Exp - 1)

Biological rep a - 8 reads

Biological rep b - 9 reads

Biological rep c - 8 reads

Sample A8 (Exp - 2)

Biological rep a - 9 reads

Biological rep b - 9 reads

Biological rep c - 9 reads

My analysis involves comparing exp 1 and exp 2 expression profiles. And i select all those reads (for each biological; Exp1 and Exp2; individually for each biological rep)

Kindly let me know if i can fix that.Or would i have to run each replicate separately in the workflow?

thanks

Karan

ADD COMMENT • link written 4.0 years ago by karanbir • 0

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