fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex
Version 1

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Workflow Type: Galaxy

Tests Passing

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.

SEEK ID: https://workflowhub.eu/workflows/857?version=1

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