User: msprindzhuk

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Posts by msprindzhuk

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How to get a .tab file with a list of mutated genes out of SNPEff in Galaxy cloud?
... How to get a .tab file with a list of mutated genes out of SNPEff in Galaxy cloud statistic HTML output? In History, can download only a HTML report (statistics output) with charts, when I go to the link with ,tab Gene file I get nothing. How to fix? ...
snpeff written 6 hours ago by msprindzhuk0
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How to preprocess .fasta genome reference, .gff3 annotation file and the input VCF to escape from the Frame Zero error with SNPEff?
... How to preprocess .fasta genome reference, .gff3 annotation file and the input VCF to escape from the Frame Zero error with SNPEff? ...
snpeff vcf gff3 annotation fasta written 2 days ago by msprindzhuk0
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What does "WARNING: All frames are zero! " mean and how to fix it when using SNPEff?
... What does "WARNING: All frames are zero! " mean and how to fix it when using SNPEff? ...
snpeff vcf data software error gff written 3 days ago by msprindzhuk0
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When running SNPEff on Galaxy on the normalized with VT tools VCF with M. Tuberculosis genome we have: WARNING: Chromosome 'gi|559794742|gb|CP003248.2|' not found
... When running SNPEff on Galaxy on the normalized with VT tools VCF with M. Tuberculosis reference built-in genome we have: WARNING: Chromosome 'gi|559794742|gb|CP003248.2|' not found. File '/home/galaxy/galaxy/database/files/000/dataset_165.dat', line 34 WARNING: Chromosome 'gi|559794742|gb|CP003248 ...
input vt vcf snpeff written 4 days ago by msprindzhuk0
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What Galaxy tools can preprocess VCF file before running the SNPEff annotation process?
... What Galaxy tools can preprocess VCF file before running the SNPEff annotation process? We have tried VT Normalize. It does not help. What are the other ways to make VCF digestable to SNPEff? ...
snpeff postprocessing vcf vt preprocessing written 5 days ago by msprindzhuk0
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Are there Java, Ruby, R, and C# APIs, wrappers for Galaxy (like blend4php)?
... Are there Java, Ruby, R, and C# APIs, wrappers for Galaxy (like blend4php)? Is there any tutorial and some code examples on how to access Galaxy`s history programmatically to fetch a processed VCF file and postprocess it on a local computer? ...
remote access wrappers api written 5 days ago by msprindzhuk0
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How to filter genome annotation results to get a report focused on specific gene mutations (positions)?
... How to filter genome annotation results to get a report focused on specific gene mutations (positions)? What formats, functions, tools, software to use? The aim is to get a list of mutation profiles of the genes responsible for drug resistance. ...
filtering annotation report positions written 7 days ago by msprindzhuk0
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How to export computation results in Galaxy cloud?
... How to export computation results in Galaxy cloud? Is it possible programmatically and all-at-once manually? What are the options and is it written in docs anywhere? ...
export written 7 days ago by msprindzhuk0 • updated 7 days ago by Jennifer Hillman Jackson21k
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What genome annotation software is available in Galaxy except SNPEff and ANNOVAR?
... What genome annotation software is available in Galaxy except SNPEff and ANNOVAR? ...
annotation cloud written 10 days ago by msprindzhuk0
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How to install ANNOVAR (annotation software) manually on a Galaxy cloud instance?
... How to install ANNOVAR manually on a Galaxy cloud instance? Is it possible only via a toolshed? ...
annovar cloud annotation written 10 days ago by msprindzhuk0

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