User: kristina.mahan

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Posts by kristina.mahan

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Comment: C: Error with gff file while building snpeff database
... 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.mahan120
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Comment: C: Error with gff file while building snpeff database
... 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.mahan120
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Comment: C: Error with gff file while building snpeff database
... 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.mahan120
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Error with gff file while building snpeff database
... 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 ...
gff snpeff java error written 8 weeks ago by kristina.mahan120 • updated 8 weeks ago by Fatima890
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Comment: 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.mahan120
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Comment: 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.mahan120
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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.mahan120
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Getting a gff file from NCBI
... 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? ...
ncbi gff written 10 weeks ago by kristina.mahan120 • updated 10 weeks ago by Arsenal20
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How do I get a gtf file to use rnaQUAST
... 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 ...
gtf ensembl gff rnaquast gencode written 11 weeks ago by kristina.mahan120
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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.mahan120

Latest awards to kristina.mahan

Popular Question 10 weeks ago, created a question with more than 1,000 views. For How to annotate chloroplast genome
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to annotate chloroplast genome
Popular Question 3 months ago, created a question with more than 1,000 views. For Issues with mapping reads onto Reference genome using bwa mem
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: k-mer finding and counting
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Popular Question 11 months ago, created a question with more than 1,000 views. For Does anybody know how to do a local install of samtools on centos without using sudo?
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