Combining DNASeq and RNASeq data

[pranjan77]

I have multiple RNASeq datasets from one plant species which does not have an assembled reference genome. But I have access to three whole genome re-sequencing(DNASeq) datasets from individuals in the same species and they are aligned to the reference genome in a close species. Any suggestions on how to get the best count for RNASeq in this scenario would be very helpful.

Thanks

[bio_informatics]

This has been cross posted at:

https://www.biostars.org/p/112537/

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