Workflows

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Showing 81 results. Use the filters on the left and the search box below to refine the results.
Type: Galaxy

Workflow Metavisitor: Trinity test in Use Case 2-2 (1)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-10-10 | Last updated: 2016-10-10

Workflow Metavisitor: Workflow for small RNA profil... (1)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server

Created: 2016-10-10 | Last updated: 2016-10-10

Workflow Sample Preparation - Remove Duplicates, Cl... (1)

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Forward and reverse raw sequencing reads are run through FastUniq (Xu et al., 2012) to remove PCR duplicates, clipped of their adapters and trimmed using Sickle (Joshi & Fass, 2011) to a minimum quality threshold of 30 and length threshold of 20. The reads are then aligned to the Drosophila Melanogaster release 6.12 reference genome (Flybase) with BWA-MEM (Li, 2013)

Created: 2016-10-02 | Last updated: 2016-10-02

Credits: User Portia Hollyoak

Workflow Filter TEMP Output files for Variant Suppo... (1)

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This workflow will take TEMP insertions and absences output files as input and filter the insertions and absences for variant support greater than or equal to 2 supporting reads.

Created: 2016-09-29 | Last updated: 2016-09-29

Credits: User Portia Hollyoak

Workflow Clip, Trim, Align to Genes and TEs, Readco... (1)

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This workflow will clip forward and reverse of their adapters and trim them using Sickle (Joshi & Fass, 2011) to a minimum quality threshold of 30 and length threshold of 20. The reads are then aligned to the Drosophila melanogaster release 6 reference genome (dm6) and to the Drosophila Transposon Sequences Canonical set v9.411 (retrieved from Ashburner et al., 2016) with Bowtie2 (Langmead & Salzberg, 2012). Featurecounts (Liao Y, Smyth GK and Shi W (2014) is then used to count reads ...

Created: 2016-09-12 | Last updated: 2016-09-12

Credits: User Portia Hollyoak

Workflow Remove Individual-specific TE insertions/a... (1)

This workflow will find insertions/absences that are specific to 3 samples (from one individual) and remove them.

Created: 2016-09-11 | Last updated: 2016-09-11

Credits: User Portia Hollyoak

Workflow Remove TE insertions/absences common to al... (1)

This workflow will take TEMP insertion files for several samples, find insertions shared between all samples, then remove them from each sample's insertion file. 

Created: 2016-09-11 | Last updated: 2016-09-11

Credits: User Portia Hollyoak

Workflow Merge and Sort Insertions produced by TEMP (1)

This workflow will take insertion files produced by TEMP and sort the insertions using SortBED and merge insertions at the same location using MergeBED.

Created: 2016-09-11 | Last updated: 2016-09-11

Credits: User Portia Hollyoak

Workflow Analysis of TE families and genes sequenci... (1)

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This workflow is used to quantify the sequencing reads mapped to gene exons within the Dm6 reference genome and the transposable element families within Drosophila Transposon Sequences Canonical set v9.411 (Ashburner et al., 2016). For each sample, the reads of the sequencing data are clipped of their adapters and trimmed to 35bp using the Trimmomatic tool (Lohse et al., 2012). The reads are then aligned to the dm6 reference genome and the  Drosophila Transposon Sequences Canon...

Created: 2016-09-11 | Last updated: 2016-09-11

Credits: User Portia Hollyoak

Workflow VCaP RNA-Seq Fusion gene detection with ST... (1)

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The end-to-end workflow starts by obtaining paired-end RNA-Seq data of the VCaP cell line via EGA. Galaxy determines the file type automatically with its built-in format detection system. The reads will be clipped before an alignment with STAR and STAR produces several output files that can be used for different analysis. The last tool is STAR-Fusion which was able to confirm the TMPRSS2-ERG fusion gene. 

Created: 2016-08-31 | Last updated: 2016-08-31

Credits: User Y. Hoogstrate

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