User: karthic
karthic • 100
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Posts by karthic
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... Thanks Juke.
Still EVM throws the following error
Fatal Error, cannot locate data entry for ID: [STRG.26026.1] at gff3_gene_prediction_file_validator.pl line 125
I just converted the gtf to gff3 with the following command
agat_convert_sp_gxf2gxf.pl -g stringtie.gtf -o stringtie.gff3
Kart ...
written 25 days ago by
karthic • 100
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... Hi,
I aligned my rnaseq to the genome using hisat2 and obtained gtf file using stringtie. Now how do i convert this gtf to EVM compatible gff3. I have checked the misc folder in the EVM software, there is no script for this.
Anyone please help
Karthic ...
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... Thanks for your quick reply.My gff3 has an attibute "gap" which has cigar like values. Below are the few lines...
HiC_scaffold_4901 gmapk15_genomeIndex cDNA_match 38678 39960 99 - . ID=Gills_HQ_transcript/28860.path1;Name=Gills_HQ_transcript/28860;Dir=indeter ...
written 5 weeks ago by
karthic • 100
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... Hi,
I have aligned my coding sequences to the genome using gmap with output format as as --gff3-match-cdna. Now I want to filter this gff3 to keep only the records having more than 90% identity.
How can i do that??
Thanks,
Karthic ...
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Comment:
C: Converting GFF to GTF
... Woww. Thats great.
Thanks for the super fast reply. ...
written 6 weeks ago by
karthic • 100
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Comment:
C: Converting GFF to GTF
... Hey Juke34,
augustus prints gff3 with UTR regions as 3'-UTR and 5'-UTR, how do I go about it?? ...
written 6 weeks ago by
karthic • 100
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... Thank you. I will check it out. ...
written 9 weeks ago by
karthic • 100
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... Thanks. I will go through that. ...
written 9 weeks ago by
karthic • 100
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... Yes, independent of the RNAseq data.
I mean gathering the evidence for the gene prediction by utilizing the RNAseq and isoseq data.
The RNAseq data should be assembled with trinity and transcripts to be given as input to tools like augustus, genemark etc or they should be mapped to genome with too ...
written 9 weeks ago by
karthic • 100
0
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... We have assembled the genome and there is no other annotation available for this species.
We have rnaseq and isoseq for some tissues. Currenlty figuring out the way I should prepare the files. ...
written 9 weeks ago by
karthic • 100
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