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?