Question: Micro-RNA Host Genes
0
gravatar for Zara_2018
28 days ago by
Zara_20180
Zara_20180 wrote:

Hi, I have carried out differential expression analysis using Deseq2. One of the most differentially expressed genes is MIR17HG - a host gene for the MIR17-92 cluster, a group of at least six microRNAs

I am wondering if this makes sense? I know micro-RNAs can't be detected in regular RNA-seq but is it correct that a non-protein coding gene is detected?

Thanks,

Zara

ADD COMMENTlink modified 28 days ago • written 28 days ago by Zara_20180
0
gravatar for Jennifer Hillman Jackson
28 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

If non-protein coding genes are included in your reference annotation, then they will be considered by DeSeq2. If you want to avoid those in your analysis, remove them from the reference annotation GTF dataset.

Galaxy tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 28 days ago • written 28 days ago by Jennifer Hillman Jackson25k
0
gravatar for Zara_2018
28 days ago by
Zara_20180
Zara_20180 wrote:

Hi Jen,

Thank you for your answer. I do not wish to exclude non-protein coding genes however I have noticed that a large proportion of my most significant differentially expressed genes are non-coding. In your experience does this point to any issue with analysis?

Thanks,

Zara

ADD COMMENTlink written 28 days ago by Zara_20180

It may be that you are not using spliced alignment settings during the mapping step.

For example, this is how to set up HISAT2 for spliced mapping (from the Galaxy Tutorials): https://galaxyproject.org/tutorials/nt_rnaseq/#spliced-mapping-with-hisat

ADD REPLYlink written 27 days ago by Jennifer Hillman Jackson25k
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