Question: DEG using edgeR script via StrandNGS
0
gravatar for rtyb91
21 days ago by
rtyb9120
rtyb9120 wrote:

Dear All,

I am a veterinarian working on a breed-specific disease with limited number of samples sent for RNA-Sequencing. As I was told that I am a biologist instead of bioinformatician, I was directed to use the commercial product StrandNGS to run analysis on my sequencing results.

There is a tutorial available by StrandNGS on this, but the tutorial is extremely vague and I literally had to figure multiple things by myself; so here's the gist of what I have done

1) Total RNA purified from colon samples of a) Control Beagles x3 b) Diseased Mucosa of paired Dachshund x3 c) Normal Mucosa of paired Dachshund was sent for sequencing using illumine HiSeq 2500 with single-read, 50bp library

2))RIN, cDNA, sequencing, and quality check was performed by the sequencing company

3) Average reads were at 20million reads

4) Reads were mapped onto the CamFam library using StrandNGS

5) Reads were filtered according to the user manual, and the samples were grouped into Beagle and Dachshund as well as Control, Diseased and Normal Mucosa

6) Normalization was done via TMM

7) Normalized reads were ran in the R editor within the built in script of StrandNGS

8) Script ran was "DEG in edgeR"

I was wondering if what I did was correct as most literature suggest edgeR to detect DEGS when replicate numbers are less than 12, and I don't think it would be correct to run the reads using normal T-test or paired T-test.

lists

I managed to get a list, with multiple columns where I have log cpm, FC, log FC, p-value, corrected p-value, regulation, and the combination of comparison amongst each of 3 groups.

What I am a little confused is while the comparisons between each of 3 groups gave me up and down regulation, the concluded log cpm, FC, log FC, p-value, corrected p-value and regulation only gave me up regulation or not significant without a down regulation. In this case, is it safe to say that I actually have a list of DEGs, but I can only see there up and down regulation using the data from the comparison between each of 3 groups?

and how would I be able to make use of the log cpm when it is all positive?

It's very confusing, even for me because it is a very unusual results I'm looking at.

Please do enlighten me if there's anyone out there who is familiar with the combined use of edgeR and StrandNGS.

rna-seq R • 130 views
ADD COMMENTlink modified 3 days ago • written 21 days ago by rtyb9120
1

Since you are paying for a license please consider contacting StrandNGS support to get help. Not many on the forum are likely to use access to or use this commercial program.

Also use these directions/image host provider to include images: How to add images to a Biostars post

ADD REPLYlink modified 21 days ago • written 21 days ago by genomax76k

Thanks for the input! I'm really trying my luck here because the accession I have is from Japan, and the support I likely to have would be in Japanese. While I am fairly well-versed in the language, I would really prefer support and inputs for the analysis in English so I wouldn't have any misunderstandings or wrong info.

So am I suppose to assume no one in the forum have any ideas how to go around this at all then?

Will be updating the image link for the main thread!

ADD REPLYlink written 20 days ago by rtyb9120

If you have a license for StrandNGS they would not mind if you contact their general support email from their contact page. You can let them know that you prefer talking with someone in English.

ADD REPLYlink modified 20 days ago • written 20 days ago by genomax76k
2
gravatar for rtyb91
3 days ago by
rtyb9120
rtyb9120 wrote:

Just to wrap things up, I finally got in touch with the StrandNGS tech support (actually they came to me first) and we managed to sort things out to proceed with more discussion via emails and zoom. Their tech support is amazing and I do recommend StrandNGS users to get in touch with then directly to sort things out in the future!

Thanks genomax for the recommendation!

ADD COMMENTlink written 3 days ago by rtyb9120

Thank you for following up on your question :)

ADD REPLYlink written 3 days ago by ATpoint28k

Thank you rtyb91!!! It was a pleasure talking to you. We will always be available to help you out!

ADD REPLYlink written 3 days ago by Strand NGS0
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