Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: HISAT2 input to StringTie with converted GFF > GTF produces error message
0
gravatar for ramibalasubramanian
9 months ago by
ramibalasubramanian • 0
ramibalasubramanian • 0 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 • 613 views
ADD COMMENT • link •
modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by ramibalasubramanian • 0
0
gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 176 users visited in the last hour