Question: HISAT2 alignment without gff files
gravatar for Olajucan
3.5 years ago by
Olajucan0 wrote:

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 • 2.7k views
ADD COMMENTlink modified 3.5 years ago by h.mon30k • written 3.5 years ago by Olajucan0

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.

ADD REPLYlink written 3.5 years ago by Sej Modha4.7k
gravatar for h.mon
3.5 years ago by
h.mon30k wrote:

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.

ADD COMMENTlink written 3.5 years ago by h.mon30k

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?

ADD REPLYlink written 3.5 years ago by Olajucan0
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