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snandiDS / prokseq-v2.0

MIT License
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Subread step fails for .gtf files produced with /scripts/gff3_2_gtf.sh #17

Open osowiecki opened 1 year ago

osowiecki commented 1 year ago

Script /scripts/gff3_2_gtf.sh creates different GTF files then your example files and later Subread fails to read these files every time. I was following your manual on this site and it can't process any downloaded sample.

//================================= Running ==================================\ || || || Load annotation file myco_tub.gtf ... || || Features : 0 || || WARNING no features were loaded in format GTF. || || annotation format can be specified using '-F'. || Failed to open the annotation file myco_tub.gtf, or its format is incorrect, or it contains no 'exon' features.

criskzimpel commented 1 year ago

Have you tried replacing "gene" from the second column with "exon", also, check if the your gtf file follows the same structure from the example gft file.

snandiDS commented 1 year ago

Hi, Sorry for the late reply. Yes, I agree with Cristina. Comparing your GTF with the example GTF will be a good idea.

On Sun, Mar 5, 2023 at 6:41 PM Cristina Kraemer Zimpel < @.***> wrote:

Have you tried replacing "gene" from the second column with "exon", also, check if the your gtf file follows the same structure from the example gft file.

— Reply to this email directly, view it on GitHub https://github.com/snandiDS/prokseq-v2.0/issues/17#issuecomment-1455155237, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANP7PT3M5LBWE4BU62HIOXTW2TF3DANCNFSM6AAAAAASEMK6TM . You are receiving this because you are subscribed to this thread.Message ID: @.***>