Workflows

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Type: Galaxy User: Portia Hollyoak

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

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