sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming)
2.0

Visit source Download RO-Crate
Workflow Type: Galaxy

This workflow completes the first part of the small RNA-seq tutorial from read pre-processing to trimming.e

Associated Tutorial

This workflows is part of the tutorial sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming), available in the GTN

Thanks to...

Tutorial Author(s): Mallory Freeberg

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1281?version=1

Steps

ID Name Description
3 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65
4 Trim Galore! toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2
5 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65
6 HISAT Alignment of reads against rRNA sequences to filter them out. toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3
7 Filter SAM or BAM, output SAM or BAM Keep reads that did NOT align to rRNA sequences. toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2
8 Convert from BAM to FastQ toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0
9 HISAT toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3
10 Filter SAM or BAM, output SAM or BAM Keep reads that did NOT align to miRNA sequences. toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2
11 Convert from BAM to FastQ toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0
12 Manipulate FASTQ toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1
13 Manipulate FASTQ toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1
14 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65
15 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65

Version History

2.0 (earliest) Created 25th Jun 2024 at 11:19 by Helena Rasche

Added/updated 4 files


Open master ae9d655
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
FastQC
Trim Galore
HISAT2
SAMtools
BEDTools
License
Creative Commons Attribution 4.0 International
Activity

Views: 450   Downloads: 109

Created: 25th Jun 2024 at 11:19

Last updated: 25th Jun 2024 at 11:19

help Attributions

None

Total size: 119 KB
Powered by
 (v.1.16.0-main)
About Dev WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH