Is using the assembled transcript in one de novo assembler as reference/trusted contigs for the second assembler logical?

Question

[RCMC]

Good day, I was playing with the settings/configuration of SPAdes and trinity in galaxy Europe (This way, I can compare which is the best for a given data sets)

I stumbled the genome guided mode in trinity and trusted contigs option in rnaSPAdes

I was thinking if any of the following methods are logical (and also to hear your thoughts?)

1. Using rnaSPAdes > use the transcript as reference to be mapped in RNA STAR > Use the BAM files in trinity genome guided mode

1. Using trinity de novo mode > use the assembled transcripts as trusted contigs for rnaSPAdes

Apologies if my thoughts do not make sense, but I have no experience in transcriptomics

In genome assembly, I usually use shovill (SKESA) and fly (If tehre are long reads) then I use this as trusted and untrusted contigs respectively to SPAdes in order to "combine the assemblies"

regards

[RCMC]

typographical correction: In genome assembly, I usually use shovill (SKESA) and flye (If there are long reads) then I use this as trusted and untrusted contigs respectively to SPAdes in order to "combine the assemblies"

[GenoMax]

Is this a eukaryote or prokaryote? What kind of data are you working with (this post is tagged RNAseq but just to be sure).

[RCMC]

I am using a eukaryotic RNA-seq (fungi specifically)

[GenoMax]

Trinity should be a good choice then. You can try to align your reads back to the assembled transcripts to see how things look rather than using these transcripts as "trusted" source for second round of assembly.