Workflows

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

AmrPlusPlus Paired Workflow (9)

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

Credits: Chris

AmrPlusPlus Single Workflow (2)

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

Credits: Chris

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: Björn Grüning

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: Björn Grüning

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

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Created: 2014-04-03

Credits: Björn Grüning

Heatmap of read coverages (1)

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Created: 2014-04-03

Credits: Björn Grüning

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: Björn Grüning

Detect ellipse failures and get votable wi... (1)

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It detects if ellipse has failed by checking if the resulting data file exists. It adds a column (validellipse) that contains 1 if ellipse didn't fail and 0 if ellipse failed. It returns a votable that contains all the data with the new column and a votable that contains only the rows where ellipse didn't failed. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/).

Created: 2012-09-07

Credits: Julian Garrido

Build plots from galfit and ellipse results (2)

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Build plots from galfit and ellipse results (http://www.myexperiment.org/workflows/3068.html, http://www.myexperiment.org/workflows/3052.html).

Created: 2012-08-30 | Last updated: 2012-09-07

Credits: Julian Garrido