FastQC or equivalent trimmomatic or equivalent Read error correction (for de novo transcriptome assembly)
redo FastQC after such steps (confirm you have removed low quality parts of reads and adapters).
It is worth noting that for SALMON, Rob Patro does not even think these QC steps are particularly necessary.
in addition to samtools checks and tools like samstat also consider
RSeQC. QC specifically for RNA seq. From their page "RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc."
qualimap. General purpose QC for sequence data with special tools for RNA-seq data.
NOISeq. General bioconductor/R library for RNA-seq, but includes a number of RNA-seq QC checks.