Transcripts mapping using Salmon
We have recently conducted total RNA-seq (~200M reads) and mRNA-seq (~100M reads) in the same samples. Following the RNA-seq, we used Salmon selective alignment (SA) to align the reads to the Ensembl human transcriptome. This resulted in a comparable number of reads (~40M) available from both RNA-seq approaches for downstream DGE analyses.
It is reasonable to think that the exon parts of a pre-mRNA will be aligned to the reference transcriptome following total RNA-seq if the length of the exons is longer than the read length. However, the Salmon SA algorithms seem to have performed well, generating comparable transcript reads and strong correlations of the DGE genes identified from the total RNA-seq and the mRNA enriched sequencing.
I have been wondering what may be the reasonable explanations for these observations above. It is appreciated if you could shed some light into this.
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