Fragmented genes

[Omicas Microbial]

Hi, I have performed my single-end data analysis using the following workflow: Tirmmomatic, Sortmerna, Trinity, Supertranscript, and Evidential Gen. However, when I make the annotations, I have noticed that some genes are fragmented into different transcripts. I would like to know what parameters I can use or change in the assembly to correct these mismatches in the sequences that are not overlapping. This is the code I am using:

 
   /media/omicas/data/apps/trinityrnaseq-v2.15.1/Trinity \

--seqType fq \

--samples_file /media/omicas/Data4/Unizar/Analisis_ppinaster_completo/samples.txt \

--CPU 30 --max_memory 200G \

--min_kmer_cov 2 \

--min_contig_length 300 \

--normalize_reads