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Showing 12 results. Use the filters on the left and the search box below to refine the results.
Type: Galaxy Tag: galaxy
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Workflow Detrprok (4)

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In the case study of stranded and prokaryotic RNAseq data, the Det'Rprok workflow detects candidates of 3 kinds of non coding RNA: 5'UTRs, antisense RNAs, and small RNAs.Inputs: i) an mapping file (bam format) containing one valid alignment by read, ii) a feature file (gff format) annotating the genomic sequences used for the mapping. Dependencies (from the Galaxy toolshed): "s_mart", "detrprok_scripts"

Created: 2013-05-20 | Last updated: 2015-11-03

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Workflow AmrPlusPlus Paired Workflow (9)

AmrPlusPlus is a Galaxy-based metagenomics pipeline that is intuitive and easy to use. The pipeline takes advantage of current and new tools to help identify and characterize resistance genes from metagenomic sequence data.

Created: 2016-08-05 | Last updated: 2016-11-18

Credits: User Chris

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Workflow AmrPlusPlus Single Workflow (2)

AmrPlusPlus is a Galaxy-based metagenomics pipeline that is intuitive and easy to use. The pipeline takes advantage of current and new tools to help identify and characterize resistance genes from metagenomic sequence data.

Created: 2016-08-12 | Last updated: 2017-01-05

Credits: User Chris

Workflow Galaxy workflow for the identification of ... (1)

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This approach screens three proteins against a given genome sequence, leading to a genome position were all three genes are located nearby. As usual in Galaxy workflows every parameter, including the proximity distance, can be changed and additional steps can be easily added. For example additional filtering to refine the initial BLAST hits, or inclusion of a third query sequence.https://github.com/bgruening/galaxytools/tree/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby

Created: 2015-03-17

Credits: User Björn Grüning

Workflow Compute and correct GC bias in NGS data (1)

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Galaxy workflow based on deepTools which will compute and correct GC bias in your NGS data. For more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03

Credits: User Björn Grüning

Workflow Heatmap of read coverages (single BAM file) (1)

Galaxy workflow based on deepTools which creates a clustered heatmap of the read coverage. One BAM file will be used as input and a heatmap will be the output.For more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03

Credits: User Björn Grüning

Workflow Heatmap of read coverages (1)

Galaxy workflow based on deepTools which creates a clustered heatmap of the read coverage. Two BAM files will be used as input and a heatmap will be the output.For more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03

Credits: User Björn Grüning

Workflow Clustered heatmap of signals around the TSSs (1)

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Galaxy workflow based on deepTools which creates a clustered heatmap of signals around the TSS. One bigwig file is needed as input with the signal and an annotation file with your TSS regions. The output will be a heatmap. You can create such a bigwig file with the bamCorrelate toolFor more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03 | Last updated: 2014-04-03

Credits: User Björn Grüning

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Workflow Gene enhancer region analysis (1)

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 This Galaxy pipeline searches for transciption factor binding sites which are conserved through to Fugu. It then finds genes associated with these enhancer binding sites. See http://screencast.g2.bx.psu.edu/MAF_manipulation for the screencast that describes how this workflow is developed.

Created: 2012-06-14 | Last updated: 2012-07-06

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Workflow Advanced FastQ manipulation (1)

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 This Galaxy workflow performs advanced FastQ manipulation as demonstrated by the screencast at http://screencast.g2.bx.psu.edu/quickie_14_fastq_adv/flow.html. Given a FastQ set of data, it will be transformed using the tools, Groomer, Filter FastQ, FastQ Trimmer, Manipulate FastQ before it is finally converted into FASTA format.

Created: 2012-06-14 | Last updated: 2012-06-14

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