Question: Differential expression from FPKM
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gravatar for Beatriz Ramos
7 months ago by
Beatriz Ramos10 wrote:

Greetings, I've been using some of galaxy tools for the last months, namely for tuxedo pipeline. I have a great amount of data so I can't leave it all on my Galaxy page to use tools like DESeq2 or even cummeRbund. Is there a way I can run any of these on R with my csv file that compiles all FPKM values? Or is there any other way to do the differential expression analysis, for exemple by using a control condition and housekeeping gene like it is done on qPCR?

Best regards

ADD COMMENTlink modified 7 months ago • written 7 months ago by Beatriz Ramos10
1
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Intermediate data can be permanently deleted from your history to make room for new analysis steps. Please see the FAQ help here:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson24k
0
gravatar for Beatriz Ramos
7 months ago by
Beatriz Ramos10 wrote:

Thank you, I already managed to make room for all my data. Can anyone tell what is the best way to do the differential expression analysis I want, knowing that I have both TopHat and HISAT outputs to combine?

ADD COMMENTlink written 7 months ago by Beatriz Ramos10
1

I personally have not tried to do this, but if the output from HISAT is set to be formatted for Cufflinks (Spliced alignment parameters > Transcriptome assembly reporting), combining both outputs might work with Cufflinks/Cuffmerge/Cuffdiff. Perhaps give this a test run?

Using Tophat output with an alternative (and best-practice workflow) using Stringtie build transcripts/merge is not recommended. Tophat is considered a deprecated tool with HISAT the update replacement.

Count-based differential expression analysis that makes use of feature counts or htseq-count as an intermediate step (example: Deseq2) seems more likely to work with the mixed BAM inputs. This would need a test, too.

RNA-seq tutorials/workflows for reference: https://galaxyproject.org/learn/

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson24k
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