User: galaxyNewbie

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galaxyNewbie10
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Posts by galaxyNewbie

<prev • 11 results • page 1 of 2 • next >
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FASTQ file split (forward and reverse not of same length)
... Is there a Galaxy package which will split a previously joined fastq which will have unequal forward and reverse lengths? FastqSplitter and similar Galaxy packages all require that the length be the same for the package to split correctly, but mine with have unequal lengths. Thank you. ...
split join trim fastq merge written 17 days ago by galaxyNewbie10 • updated 17 days ago by Jennifer Hillman Jackson25k
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Removal of primers using Trimmomatic
... Hello, Trimmomatic has an illuminaClip feature which appears to be able to cut custom sequences (i.e. primers, adapters) from one's sequence. I designated the custom adapter, but the adapter is still present after I run the trimmomatic command. I should not see those unwanted and supposedly but p ...
trimmomatic fastqsanger.gz primers written 21 days ago by galaxyNewbie10 • updated 20 days ago by Jennifer Hillman Jackson25k
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Conversion of a .vcf (variant control format) to a .maf (mutation annotation file)
... Hello, Is there a galaxy package which will convert a .vcf to a .maf (mutation annotation file)? I didn't see vcf2maf as an available package. Thank you. ...
maf vcf maftools vcf2maf development written 4 weeks ago by galaxyNewbie10 • updated 4 weeks ago by Jennifer Hillman Jackson25k
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(Closed) convert annovar in excel to vcf for igv viewing
... Hello, In an excel file I have the chromosome, start and stop positions, reference allele (Ref), alternate.(alt) and numerous annovar scores. How do I convert this excel into a .VCF file so that I can view it in IGV or another genomic viewer? Please let me know if I can provide any additional det ...
annovar igv vcf excel format written 4 weeks ago by galaxyNewbie10 • updated 4 weeks ago by Jennifer Hillman Jackson25k
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Comment: C: Galaxy fastqc contaminant list
... Thank you Jen. Importing the primer/adapter list as a tabular file was successful. ...
written 11 weeks ago by galaxyNewbie10
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Galaxy fastqc contaminant list
... Hello...I created a tab separated text file containing a primer name and associated primer sequence, but Galaxy's factqc does not seem to recognize my tab delimited text file format. 1. Is the format .txt (tab delimited)? 2. I only have two columns, the primer name and associated sequences. Than ...
input contaminant fastqc tabular fastq written 11 weeks ago by galaxyNewbie10 • updated 11 weeks ago by Jennifer Hillman Jackson25k
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Changing file_path to local database/files directory
... 1. galaxy.ini has the default file path set to database/files. Since I have a local instance of galaxy installed I presumed this was in my local database/files directory, but I only see a .dat file in this directory. Since I would like to store my uploaded files in my local directory should this ...
galaxy.ini local config upload admin written 5 months ago by galaxyNewbie10 • updated 5 months ago by Jennifer Hillman Jackson25k
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Continuous processing for jobs where metadata is auto-detected
... I have a local installation of galaxy. I designated that my job "auto-detect metadata." The job has been running for several days (yellow highlight with wheels turning) without completion. There is another posting "Metadata Is Being Auto-Detected Stuck In Continuous Loop" which describes my sa ...
autodetect metadata datatype format written 5 months ago by galaxyNewbie10 • updated 5 months ago by Jennifer Hillman Jackson25k
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Configure file path for storing datasets
... Hello, How can I change the file path for storing my datasets? Do I need to change this in the galaxy.ini? If so, how do I change the #file_path ? I just want to store my datasets in a different location (I believe) than galaxy's default. Thank you! ...
file_path storage galaxy.ini written 5 months ago by galaxyNewbie10 • updated 5 months ago by Jennifer Hillman Jackson25k
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Comment: C: Access to files uploaded using Admin (local instance)
... Thanks for the response ! To configure the storage file path, do you set this in galaxy.ini? It appears you can set the file_path for the location as to where the datasets are stored, but I'm not certain where to change that location. ...
written 5 months ago by galaxyNewbie10

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