Workflow Type: Galaxy
Frozen
This workflow takes a collection of BAM (output of STAR) and a gtf. It extends the input gtf using de novo annotation.
Inputs
ID | Name | Description | Type |
---|---|---|---|
BAM collection | #main/BAM collection | BAM collection for example output of STAR |
|
Input gtf | #main/Input gtf | n/a |
|
minimum FPKM for merge | #main/minimum FPKM for merge | n/a |
|
minimum coverage | #main/minimum coverage | n/a |
|
strandedness | #main/strandedness | n/a |
|
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+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
extended_gtf | #main/extended_gtf | n/a |
|
Version History
v0.1 (earliest) Created 20th Jun 2024 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
1578b3f
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Views: 516 Downloads: 95 Runs: 0
Created: 20th Jun 2024 at 03:02
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