User: karthic

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karthic100
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Posts by karthic

<prev • 73 results • page 1 of 8 • next >
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Comment: C: How do I convert Hisat2 + stringtie gtf to EVM compatible gff3
... 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 karthic100
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How do I convert Hisat2 + stringtie gtf to EVM compatible gff3
... 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 ...
gene prediction rna-seq written 26 days ago by karthic100 • updated 25 days ago by Juke344.9k
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Comment: C: Filter gmap GFF3 output by identity
... 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 karthic100
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Filter gmap GFF3 output by identity
... 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 ...
genome gmap gene prediction written 5 weeks ago by karthic100 • updated 5 weeks ago by Juke344.9k
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Comment: C: Converting GFF to GTF
... Woww. Thats great. Thanks for the super fast reply. ...
written 6 weeks ago by karthic100
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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 karthic100
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Comment: C: Alignng RNAseq data for gene prediction
... Thank you. I will check it out. ...
written 9 weeks ago by karthic100
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Comment: C: Alignng RNAseq data for gene prediction
... Thanks. I will go through that. ...
written 9 weeks ago by karthic100
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Comment: C: Alignng RNAseq data for gene prediction
... 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 karthic100
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Comment: C: Alignng RNAseq data for gene prediction
... 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 karthic100

Latest awards to karthic

Popular Question 2.1 years ago, created a question with more than 1,000 views. For Genome size estimation using jellyfish
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Any methods available to do QC analysis of Pacbio raw data??
Scholar 2.2 years ago, created an answer that has been accepted. For A: perl script for discarding sequences less than 200 nucleotides before running C
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: perl script for discarding sequences less than 200 nucleotides before running C
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Any methods available to do QC analysis of Pacbio raw data??

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