Admin: genomax

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genomax90k
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Posts by genomax

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Answer: A: TAIR Gene Symbols
... Using [EntrezDirect][1]: $ esearch -db gene -query "Arabidopsis thaliana [ORGN]" | efetch -format tabular | head -5 tax_id Org_name GeneID CurrentID Status Symbol Aliases description other_designations map_location chromosome genomic_nucleotide_accession.version start_position_on_the_genomi ...
written 1 hour ago by genomax90k
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Comment: C: truth vcf NA12878.NIST reference
... Should be the entire genome based on the name. Did you peek inside the file to see what is there? ...
written 1 hour ago by genomax90k
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Comment: C: How would I use BioPython to mass download some assemblies from NCBI?
... $ ./datasets assembly-descriptors taxon "Neophocaena asiaeorientalis" {"assemblies":[{"assembly":{"annotation_metadata":{"file":[{"estimated_size":"13363717","type":"GENOME_GFF"},{"estimated_size":"966592048","type":"GENOME_GBFF"},{"estimated_size":"24351233","type":"RNA_FASTA"},{"estimated_ ...
written 3 hours ago by genomax90k
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Comment: C: How would I use BioPython to mass download some assemblies from NCBI?
... EDIT: Curiously using the fully qualified accession number (with version) works fine, so that error message is not appropriate (accession number per se is not invalid): $ ./datasets download assembly GCF_003031525.1 Downloading: ncbi_dataset.zip 836kB 1.12MB/s So someone must be doing a ...
written 3 hours ago by genomax90k
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Comment: C: How would I use BioPython to mass download some assemblies from NCBI?
... There is an explanation of what is excluded at the link you included above. So they are not doing this without telling users. They also tell the users where the `missing` excluded genomes can be found. This is one additional tool like the others mentioned in this thread. It comes with its own limit ...
written 4 hours ago by genomax90k
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Answer: A: How would I use BioPython to mass download some assemblies from NCBI?
... Since non-python solutions have been mentioned, consider [NCBI datasets][1]. It is the command line tool for downloads of genomic data from NCBI. Note: Limited to eukaryotic genomes via the web interface and to other constraints mentioned at the link posted by @Istvan in comment below. [1]: htt ...
written 4 hours ago by genomax90k
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Comment: C: content negotiation for the ontobee sparql endpoint
... Cool. If you get an answer there come back and update this thread with it. Would help someone in future. ...
written 9 hours ago by genomax90k
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Comment: C: content negotiation for the ontobee sparql endpoint
... Would posting to Ontobee [google group][1] be easier/appropriate? [1]: http://www.ontobee.org/contactus ...
written 9 hours ago by genomax90k
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Comment: C: De novo transcriptome from PE reads with high multi-mapping rate (Bowtie2)
... > Is it correct that one mustn't put too much stock into the > transcript-level expression metrics? In this case, since the transcriptome is new and not well characterized. It also does not have the support of genomic sequence. ...
written 10 hours ago by genomax90k
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Comment: C: Using gffread to extract annotated fasta sequences from a genome
... If this feature is indeed missing from new version you may want to create an issue on their dev site and request that it be put back. ...
written 10 hours ago by genomax90k

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