brew3r/main

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Workflow Type: Galaxy

This workflow takes a collection of BAM (output of STAR) and a gtf. It extends the input gtf using de novo annotation.

SEEK ID: https://workflowhub.eu/workflows/1051?version=2

Inputs

ID Name Description Type
BAM collection #main/BAM collection BAM collection for example output of STAR
  • array containing
    • File
Input gtf #main/Input gtf n/a
  • File
minimum FPKM for merge #main/minimum FPKM for merge n/a
  • float
minimum coverage #main/minimum coverage n/a
  • int
strandedness #main/strandedness n/a
  • string

Steps

ID Name Description
5 Map parameter value toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
6 Unstranded toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
7 assembl with StringTie toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0
8 merge assembled transcripts toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0
9 BREW3R.r toolshed.g2.bx.psu.edu/repos/iuc/brew3r_r/brew3r_r/1.0.2+galaxy1

Outputs

ID Name Description Type
extended_gtf #main/extended_gtf n/a
  • File

Version History

v0.2 (latest) Created 10th Oct 2024 at 03:02 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 831d065

v0.1 (earliest) Created 20th Jun 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 1578b3f
help Creators and Submitter
Creator
  • Lucille Delisle
Submitter
Tool
StringTie
License
GNU General Public License v3.0 or later
Activity

Views: 1068   Downloads: 191   Runs: 0

Created: 20th Jun 2024 at 03:02

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