I first used hisat2 and successfully align the SRA sequence to the reference genome, then used stringtie for the annotation. The script is as follow:
The code run smooth without any error generated, however, the product from stringtie is in fastq format instead of gtf. May I know is there any mistake in my script that make the gtf file cannot be produced?
Many thanks!
The code run smooth without any error generated, however, the product from stringtie is in fastq format instead of gtf. May I know is there any mistake in my script that make the gtf file cannot be produced?
Many thanks!