This is a test version of Biostars. For the public version, visit https://www.biostars.org.
HISAT2 alignment without gff files

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?

rna-seq alignment
• 5,736 views • link
updated by h.mon h.mon • written by Olajucan • Olajucan

1 answer

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.

• 0 views • link
written by h.mon h.mon

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?

• 0 views • link
written by Olajucan • Olajucan

Log in to answer this question.

More posts like this