I map pair end reads to genome using Hisat2 and sam file was sort and converted in bam file.

After that I used this command for StringTie assembly:

/home/yog/software/stringtie-1.3.2.Linux_x86_64/stringtie -p 8 -G gene.gtf -o assembly.gtf -m 500 -v map.bam

It creates these following files:

1) assembly.gtf 2) t_data_ctab 3) i2t_ctab 4) i_data_ctab 5) e2t_ctab 6) e_data_ctab

then through gffread I extracted assembled fasta sequences, using reference.fasta

/gffread assembly.gtf -w transcript.fasta -g reference.fasta

Is it the right way to do genome-guided assembly using StrinTie?

Can I get assembled fasta sequence directly from the above stringTie command?

Thanks in advance