fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex
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Tests Comprehensive preprocessing for 10X Genomics CellPlex multiplexed single-cell RNA-seq data. Processes Cell Multiplexing Oligo (CMO) FASTQ files with CITE-seq-Count including required CellPlex-specific translation steps. Simultaneously processes gene expression FASTQ files with STARsolo and DropletUtils for alignment and cell filtering, and formats outputs for seamless import into Seurat/Scanpy (Read10X function).
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/9.5+galaxy0 |
| 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
v0.6.2 (latest) Created 26th Mar 2025 at 09:52 by WorkflowHub Bot
Updated to v0.6.2
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v0.6.25c103e7
v0.1 (earliest) Created 22nd Dec 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
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v0.1
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Views: 4691 Downloads: 1038 Runs: 0
Created: 22nd Dec 2023 at 03:01
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