User: kristina.mahan
kristina.mahan • 120
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Posts by kristina.mahan
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... If I am using a gff file- I have to put -gff3 in the build command. Also - I used -gffs to build the database for the nuclear genome and it worked. Something seems to be wrong with the gff files themselves but just haven't figured it out. ...
written 8 weeks ago by
kristina.mahan • 120
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... What do you mean read? I just entered the build command to build the database`11. java -jar snpEff.jar build -gff3 -v scenedesmus_obliquus_doe0152z_mitochondria`
Oh maybe its the -gff3? Except I used the same thing to build the database for the nuclear genome . . . ...
written 8 weeks ago by
kristina.mahan • 120
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... It's the same path I used for the nuclear genome (except folder was scenedesmus_obliquus_doe0152z_nuclear/genes.gff). And same way that it was done here: https://www.biostars.org/p/50963/#51165
I cd's using the path you listed (/home/kmmahan/snpEff/./data/scenedesmus_obliquus_doe0152z_mitochondria) ...
written 8 weeks ago by
kristina.mahan • 120
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... I built a snpEff database for my nuclear genome. It worked. I am now trying to build own for the chloroplast and mitochondria genomes. I've edited the config file and I have fasta files in the genome folder and their corresponding .gff files in their respective folders. I'm getting this error after ...
written 8 weeks ago by
kristina.mahan • 120
• updated
8 weeks ago by
Fatima • 890
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C: Getting a gff file from NCBI
... I have some variants I want to annotate using snpEff in the chloroplast genome. I need a gff file. ...
written 10 weeks ago by
kristina.mahan • 120
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C: Getting a gff file from NCBI
... This is the same strain. How can I convert it to a gff file? ...
written 10 weeks ago by
kristina.mahan • 120
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Comment:
C: Getting a gff file from NCBI
... https://www.ncbi.nlm.nih.gov/nuccore/NEDT01000001.1
I don't see how I can get the gff file ...
written 10 weeks ago by
kristina.mahan • 120
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... I am looking for the gff file for the chloroplast of Tetradesmus obliquus strain DOE0152z. Why is it so hard to find on NCBI? Can somebody point me in the right direction please? ...
written 10 weeks ago by
kristina.mahan • 120
• updated
10 weeks ago by
Arsenal • 20
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... I want to run rnaQUAST on my transcriptome assembly on a yellow green algae. rnaQUAST says it needs a transcripts fasta file, genome assembly fasta file, and a gene coordinates gtf file from Ensembl or Gencode. Do I just try to find the closest related organism to my organism or how do I go about th ...
written 11 weeks ago by
kristina.mahan • 120
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Comment:
C: Blobtools output files
... entire assembly is ~2000 contigs.
no-hits: 594 contigs
Bacteria: 252 contigs
Proteobacteria: 817 contigs
Haptista: 6 contigs
Chordata: 17 contigs
Euglena: 1 contig
Ascomycota: 3 contigs
Streptophyta: 7 contigs
Chlorobi: 1 contig
Chlorophyta: 36 contigs
Most all the Proteobacteria have the same GC ...
written 3 months ago by
kristina.mahan • 120
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