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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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Question about RNA prep kit supported by DCC #55

Closed giuseppe0525 closed 6 years ago

giuseppe0525 commented 6 years ago

Hi,

I want to enquire if the RNA prep kit TruSeq Stranded mRNA Sample Prep Kit is supported by DCC. Is there any evidence supporting this idea?

According to the chapter Deep Computational Circular RNA Analytics from RNA-seq , the first-strand kit TruSeq Stranded mRNA Sample Prep Kit is available for DCC (explained below). However, as far as I know, the TruSeq Stranded mRNA Sample Prep Kit employs poly-T oligo attached magnetic beads to purify the poly-A containing mRNA, suggesting that the cirRNAs, which lack the poly-A terminal, will be depleted with this procedure.

“DCC supports different sequencing protocols widely used for whole-transcriptome experiments. … The following list gives an overview of common sequencing kits and the respective parameter choice: First-strand kits (default): ●● All dUTP methods, NSR, NNSR ●● TruSeq Stranded Total RNA Sample Prep Kit ●● TruSeq Stranded mRNA Sample Prep Kit ●● NEB Ultra Directional RNA Library Prep Kit ●● Agilent SureSelect Strand-Specific”

Thank you in advance.

giuseppe

tjakobi commented 6 years ago

Dear @giuseppe0525,

you are correct, the "TruSeq Stranded mRNA Sample Prep Kit" should not appear in this list due to the reason you mentioned. Generally, the kit should work with total RNA and not select for poly-A, as this would filter out probably all circRNAs.

Cheers, Tobias

giuseppe0525 commented 6 years ago

Thanks for your answer.