query on Salmon mapping to mRNAs

[Guan Wang]

Hi,

Following the Salmon mapping, the reads obtained from mRNA-seq (no further treatment) and total RNA-seq (treated with rRNA depletion and globin mRNA reduction) should theoretically be comparable as both mapped to mature mRNAs for DGE analysis, assuming sufficient reads generated. Is this interpretation correct? Or the exon counts following Salmon mapping may be still aggregated given both the spliced and unspliced RNA species? which I would assume not.

Please note that in both experiments, large amount of raw reads were generated (>100M reads), which should circumvent the need for globin mRNA reduction in the mRNA-seq for the cross-platform comparison between the two RNA-seq platforms.

Thanks

Guan