Workflow Type: Galaxy
Frozen
This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.
Steps
ID | Name | Description |
---|---|---|
8 | process GEX reads | n/a |
9 | CITE-seq-Count | toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0 |
10 | Rename STAR-solo output | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
11 | translate 10x barcode v2 to 10x barcode v1 | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
12 | Re-organize CITE-seq-Count output | n/a |
13 | rename CITE-seq output | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
Version History
v0.5 (earliest) Created 26th Sep 2024 at 03:02 by WorkflowHub Bot
Updated to v0.5
Frozen
v0.5
799abbb
Creators and Submitter
Creators
Submitter
Tool
License
Activity
Views: 34 Downloads: 6 Runs: 0
Created: 26th Sep 2024 at 03:02
Tags
This item has not yet been tagged.
Attributions
None