Question: Processing Multiple FastQ files to obtain an expression matrix
gravatar for danhollern
4.6 years ago by
United States
danhollern0 wrote:



As a learning experience I am playing around with RNA Seq fastQ data. My goal is to simply obtain matrix of gene expression values for each sample that I say go forward and cluster. 

I am looking for recommendations on a workflow to use to achieve this. 


I have never done this before, but based on my limited understanding, I am thinking I need to do the following:

Pre-process using fastqc, and aligning using tophat, and then use cufflinks to obtain expression values.


One main concern I have is running FASTqc on multiple samples/files at the same time. Is this possible?


Like I said, I am really new at this and trying familiarize myself, so any guidance/feedback is greatly appreciated.





rna-seq galaxy • 1.5k views
ADD COMMENTlink modified 4.6 years ago by Jennifer Hillman Jackson25k • written 4.6 years ago by danhollern0
gravatar for Jennifer Hillman Jackson
4.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


You will want to run FastQC on each sample, but you can execute it in batch. 

1 - have all of the input data in one history

2 - create a workflow that contains at least an "Input" step and the "FastQC" step

3 - when running the workflow, click on the icon that looks like a little stack of files on the Input step. This will allow you to select multiple files.

4 - the workflow will execute on each of the files.

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink written 4.6 years ago by Jennifer Hillman Jackson25k
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