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stringTie is just looking at clumps of alignments and how they might relate to each other (either due to spliced alignments or proximity). Trinity is doing the more computationally difficult task of finding parts of reads that overlap with each other and trying to link them together into longer sequences.

Transcript expression level, refers to how abundant a transcript is, i.e. if a certain mRNA (a transcript) exist in many or few copies (expression level).

Stringtie Merge txt is a text file “manifest” with a list (one per line) of GTF files that you would like to merge together into a single GTF file. –rf tells StringTie that our data is stranded and to use the correct strand specific mode (i.e. assume a stranded library fr-firststrand).

The transcriptome assembly process assigns each new transcript a unique name so that it can be differentiated within the assembly. This means that the high- and low-quality assemblies do not share identical transcripts or names common to both assemblies, making the direct comparison of sequences impossible.

gtf> StringTie outputs a file with the given name with all transcripts in the provided reference file that are fully covered by reads (requires -G).

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.