User: mcrabtree

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mcrabtree10
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2 weeks, 1 day ago
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3 weeks, 4 days ago
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m********@mcw.edu

Posts by mcrabtree

<prev • 5 results • page 1 of 1 • next >
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Subtract one data set from another
... Is there a text manipulation tool or other tool that allows subtraction upon a data set by another data set that is aligned? For example, if a defined column in two data sets were: File #1: A,B,C,D,E,F,G,H,I,J,K,L,M File #2: B,D,K,L [File #1] - [File #2] = A,C,E,F,G,H,I,J,M This shouldn't be t ...
cut filter subtract text-manipulation merge written 15 days ago by mcrabtree10 • updated 15 days ago by Jennifer Hillman Jackson24k
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Comment: C: ANNOVAR v0.2 on local server has no reference databases
... I fetched the genome from NCBI directly using the "Retrieve FASTA from NCBI (Galaxy Version 1.1.0)" tool. Here's what I see under admin --> local data --> all fasta: [value] [dbkey] [name] [path] [hg19] [hg19] [Human (Homo sapiens) (b37): hg19] [/galaxy/data/hg19/seq/hg19.fa] Regarding the ...
written 16 days ago by mcrabtree10
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Comment: C: ANNOVAR v0.2 on local server has no reference databases
... Yes, I have fetched the FASTA file for GRCh37, which retrieved 3,348 sequences. Beyond that, I'm not sure how to use that file, or if I need to reference it somewhere. For the annovar.loc file, I have entered the following: hg19 hg19 hg19 [Human Feb. 2009 (GRCh37/hg19)] /export/annovar/a ...
written 16 days ago by mcrabtree10
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Comment: C: ANNOVAR v0.2 on local server has no reference databases
... Thanks for your response. I have made some progress, but I'm not quite there yet. Here are where things stand -- I successfully downloaded some databases using annotate_variation.pl -downdb -buildver [-webfrom annovar] . I also located the tool-data/annovar.loc file and updated it as follows: hg ...
written 17 days ago by mcrabtree10
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ANNOVAR v0.2 on local server has no reference databases
... Hello, I recently used "ANNOVAR Annotate VCF with functional information using ANNOVAR (Galaxy Version 0.2)" on usegalaxy.org using the following settings: For gene annotations, I entered: refGene, gencodev19 For annotation regions, I entered: GenomicsSuperDups, phastConsElements46way For annotati ...
index local annovar data reference written 18 days ago by mcrabtree10

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