Is there any tool to combine CAGE-seq data, Iso-seq data and RNAseq data?

Question

[freddiejung]

Hi, currently, I am trying to build an accurate transcript model of non-model species.

I have performed CAGE-seq, Iso-seq and strand specific RNA-seq on the same sample.

The problem is, the Iso-seq library kit my service provider used did not employ 5' cap selection.Thus, 5' sequences of my Iso-seq data were incomplete.

Now, I am wondering if CAGE-seq and strand-specific RNA-seq data could complement the Iso-seq data.

However, so far I have not found tools which can integrate CAGE-seq and other seq data.

Is there any tool to combine CAGE-seq data, Iso-seq data and RNAseq data?

Any suggestions would be appreciated.

Thanks, freddiejung

Answer 1

[Charles Plessy]

I do not have a full solution but in the CAGEr Bioconductor package you can cluster the CAGE signal and extract the coordinates of the dominant peak for each cluster. These dominant peaks might be used to extend or trim the transcript models that have their 5′ end within an arbitrary threshold.

https://bioconductor.org/packages/release/bioc/vignettes/CAGEr/inst/doc/CAGEexp.html#ctss-clustering