User: Björn Grüning

gravatar for Björn Grüning
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4 years, 8 months ago
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6 years, 7 months ago
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b**************@pharmazie.uni-freiburg.de

Posts by Björn Grüning

<prev • 32 results • page 1 of 4 • next >
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Answer: A: Chip-Seq Normalization To Total Number Of Reads
... Hi Catheryn, for ChIP-seq analysis, normalisation and BAM file correlation we use deeptTools. Here you can read more about it: https://github.com/fidelram/deepTools And here is the toolshed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools Cheers, Bjoern ...
written 4.7 years ago by Björn Grüning350
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Answer: A: Blast On Galaxy?
... Hi Jorge, Yes! Yes! Yes! But you need a local Galaxy instance, or a Galaxy instance where you can convince the administrator to install the Blast Tools. To install the Blast tools you can use the Tool Shed: http://wiki.galaxyproject.org/Tool%20Shed Here is the repository: http://toolshed.g ...
written 4.7 years ago by Björn Grüning350
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Answer: A: Trackster Error: Needlargemem: Trying To Allocate 0 Bytes (Limit: 100000000000)
... Hi Simon, I had that error before, not with trackster ... somewhere else. I think it's an error of one of these UCSC tools and it occurs if you supply empty files. Can you check that none of your file is empty? Or your file will be automatically converted during trackster visualisation and that is ...
written 4.8 years ago by Björn Grüning350
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Answer: A: Problem Running Augustus
... Hi Claudio, did you installed Augustus with the ToolShed? The env variable $AUGUSTUS_SCRIPT_PATH need to be set and point to the augustus wrapper folder containing the extract_features.py script. Hope that helps! Bjoern ...
written 4.8 years ago by Björn Grüning350
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Answer: A: Rna-Dna Converter In Fasta Format
... Hi Thanh, under "FASTA manipulation" I have one tool das is called "RNA/DNA converter". If it is not available in your instance you need to install the FASTX-toolkit wrappers. These are available in the Tool Shed. Hope that helps, Bjoern ...
written 4.9 years ago by Björn Grüning350
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Answer: A: Fwd: About Empty No Peek Problem
... Hi Xiao, can you show us the complete wrapper XML script? Thanks, Bjoern ...
written 5.0 years ago by Björn Grüning350
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Comment: C: Illumina Methylation Tool In Toolshed
... Not that I know of, mine is wrapping IMA. cheers, Bjoern *http://www.bioconductor.org/packages/2.12/bioc/html/lumi.html https://github.com/bgruening/galaxytools/tree/master/illumina_methylat ion_analyser ...
written 5.0 years ago by Björn Grüning350
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Answer: A: Illumina Methylation Tool In Toolshed
... Hi Sachit, not in the toolshed but you can find a start here: https://github.com/bgruening/galaxytools/tree/master/illumina_methylat ion_analyser its for the 450k chips, I have also some tools for WGMA if you are interested. Cheers, Bjoern ...
written 5.0 years ago by Björn Grüning350
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Answer: A: Galaxy Error
... Hi Toni, to convert a bed file to a fasta file you need the genomic sequence. You can specify a genome-build for every bed file in your history. You probably don't have a genome build specified or its specified as sacCer2. sacCer2 is not configured I would guess, so no genome is available. Try to i ...
written 5.1 years ago by Björn Grüning350
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Answer: A: Regarding Galaxy Wrappers: "Lumi", "Deseq" "Edger"
... Hi Sachit, we are working currently on a DESeq2 wrapper. Not yet finised sorry. There is also a edgeR Test repository from Ross Lazarus under: http://testtoolshed.g2.bx.psu.edu/view/fubar/edger_test Work is in progress, help is welcome! Ciao, Bjoenr ...
written 5.1 years ago by Björn Grüning350

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