HISAT2 alignment without gff files

Question

[Olajucan]

I'm new to bioinformatics and having problems with RNAseq analysis.

I'm trying to use HISAT2 to align RNAseq reads to wheat genome.

Since wheat reference genome was released in Jan., I could align my sequences to the genome.

However, GFF file for this reference is not yet built, so I can't quantify transcripts.

Are there any ways to build GFF file in this situation?

Or, do I have to perform de novo assembly?

[Sej Modha]

HISAT2 does not require a GFF or GTF file but these annotation files will be needed at a later stage of analysis if you want to run count based or FPKM pipelines.

https://ccb.jhu.edu/software/hisat2/manual.shtml

Answer 1

[h.mon]

You can use StringTie to construct a "reference" transcriptome and then Ballgown or CuffDiff to quantify transcripts. Of course, you will have to annotate the transcriptome as well.

[Olajucan]

h.mon, Thank you for your answer. Then how can I get fasta files from StringTie constructed reference? I need fasta files to annotate my transcripts, right?