I have a paired-end RNA-Seq file. I have used HISAT2 to map it against my reference genome and obtained a BAM file in result. Then, I used Stringtie to run the BAM files and obtained a gff file of the different genes expressed. However, I want the transcript or CDS sequence exactly pertaining to the genes enlisted in gff file. Is there any option of obtaining that? I want an assembled transcriptome sequence file containing all the sequences mapped to the genome. I tried de novo assembly but that assembly does not show the desired gene sequence I am looking for which i got in the gff file.
This tutorial has a sub-step that describes how to use gffread to extract predicted reference transcripts based on a GTF reference annotation.
Please see the step here → Hands-on: Genome-wide alternative splicing analysis / Genome-wide alternative splicing analysis / Transcriptomics
Hope this helps!