The sample used for sequencing was ssDNA viral particles sequenced on MiSeq PE250. The sample was initially mapped to a viral vector genome with a mapping rate more than 96%. I wish to find what RNA molecules and non-AAV DNA molecules are present in the Sample. So to achieve this the sample was again sequenced using mRNA library kit. This sequencing was done for PE150 on HiSeq. The reads obtained were de novo assembled usign SPAdes and BLASTed against NCBI.
Also, the unmapped reads from the ssDNA library were
de novo assembled and BLASTed against NCBI.
Is this a correct approach to identify RNA or non-AAV DNA contamination in the Sample. What other tools/programmes can I use for the same purpose?