Question: HISAT2 input to StringTie with converted GFF > GTF produces error message
0
gravatar for ramibalasubramanian
3 months 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 • 194 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by ramibalasubramanian0
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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: https://biostar.usegalaxy.org/p/26873

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 98 users visited in the last hour