Question: HISAT2 input to StringTie with converted GFF > GTF produces error message
gravatar for ramibalasubramanian
18 days ago by
ramibalasubramanian0 wrote:

i tried stringtie by giving the hisat2 output, it was showing error. then i tried converting my refseq .gff to .gtf using gffread. after using gffread i got one output in .gtf format but nothing was written in the file. Help me with this

gff gff3 gtf stringtie hisat2 • 45 views
ADD COMMENTlink modified 16 days ago by Jennifer Hillman Jackson24k • written 18 days ago by ramibalasubramanian0
gravatar for Jennifer Hillman Jackson
16 days ago by
United States
Jennifer Hillman Jackson24k wrote:


GFF3 datasets cannot be directly converted to GTF format with the tool you are using.

Instead, obtain a valid GTF file for your target genome. Many are at iGenomes. Please see this prior post for details:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 16 days ago by Jennifer Hillman Jackson24k
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