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Tests Extends 3' ends of gene annotations using BAM files (from STAR alignments) and a reference GTF. Specifically designed for 3'-biased sequencing techniques like 10X scRNA-seq or BRB-seq that primarily capture transcript 3' ends. The BREW3R tool enhances annotations by using evidence from RNA-seq data to improve 3' UTR definitions, which is particularly important for accurate quantification in single-cell and bulk RNA-seq experiments.
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/3.0.3+galaxy1 |
| 8 | merge assembled transcripts | toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/3.0.3+galaxy1 |
| 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 |
|
Version History
v0.1 (earliest) Created 20th Jun 2024 at 03:02 by WorkflowHub Bot
Updated to v0.1
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v0.11578b3f
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Views: 5595 Downloads: 22222 Runs: 0
Created: 20th Jun 2024 at 03:02
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