RNA secondary structure with DNA data

Question

[Alaki]

Hello there,

As you have already read the title of my question; Is it possible to do RNA secondary structure prediction study with whole genome DNA-seq data instead of RNA-Seq?

The DNA-data are from human and they are sequenced by llumina pair-end library preparation.

[Ram]

Possible details that might help your question make sense:

1. specifics on the data you have ("DNA sequence data" is highly vague)
2. how you obtained this data - the experiments you conducted, the pipelines you used, etc.
3. what aspect of RNA structure you're looking to study

[Alaki]

Just updated it! hopefully make more sense now.

[Ram]

I'm sorry, but it doesn't. Like genomax2 says, how have you processed this data? Are these just reads, or have they been aligned to the ref genome, or have they been assembled de novo? And why are you looking to obtain RNA structure data from DNA short read sequencing results?

[GenoMax]

Still not clear if you want to do this analysis with individual reads or with something longer in length (assembled contigs?).

[spvensko]

You would need information about transcript isoforms which cannot be obtained from DNA-seq data.