Question: Using STAR and DESeq2 for circRNA analysis
0
gravatar for csijst
7 months ago by
csijst0
Singapore/National University of Singapore
csijst0 wrote:

Hi,

I noticed a group that went for the ASH conference presented a poster, being able to conduct differentially expressed circRNAs using STAR and DESeq2 (https://ash.confex.com/ash/2018/webprogram/Paper113333.html). But from my understanding, rRNA depleted samples may not be able to present as accurate analysis of circRNA because linear mRNAs are still viable in the pool.

This brings me to 3 questions:

1) So DESeq2 is able to analyze circRNA? 2) But DESeq2 uses count method for analysis. Could it be then less sensitive as to algorithms such as Sailfish-cir? 3) Am I right to say that DESeq2's analysis on total RNA/rRNA depleted samples are considered a consolidation of any fragments that are covered within the regions/cluster of reads?

Thank you.

Regards, Johann

deseq2 star • 169 views
ADD COMMENTlink modified 7 months ago by Michael Love25k • written 7 months ago by csijst0
Answer: Using STAR and DESeq2 for circRNA analysis
0
gravatar for Michael Love
7 months ago by
Michael Love25k
United States
Michael Love25k wrote:

I'm not really an expert on circRNA analysis. I'd recommend contacting the authors of that poster.

ADD COMMENTlink written 7 months ago by Michael Love25k
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