I am trying to convert fasta file of the transcripts to gtf using a reference genome, but I am having some trouble. I specifically need gtf file of mRNA to run a program. The genome and the transcript data were downloaded from (https://parasite.wormbase.org/ftp.html). Following are the approaches I have taken so far:
- fasta-to-gtf script (https://github.com/willblev/fasta-to-gtf)
I found a script converts fasta files to gtf using a reference genome file, but I keep getting a syntax error below. I checked the script and could not identify or manipulate the syntax problem in line 3.
./fasta-to-gtf.py: line 3: syntax error near unexpected token `(' ./fasta-to-gtf.py: line 3: `def usage():'
- Alignment using hisat2
I tried to align the transcript file to the genome using hisat2. However, I'm not sure how to run hisat2 with the transcript file. I tried to use the transcript.fasta and genome.fasta as mate 1 and mate 2 with the index generated from annotation file, but I received the error below. The only fix I found was on bowtie2 github that suggests redownloading the latest version of the program, but I am already using the latest version of hisat2 (https://github.com/BenLangmead/bowtie2/issues/149).
Segmentation fault (core dumped) (ERR): hisat2-align exited with value 139
Please let me know if you have any other suggestions on this conversion process and if you need any further information.