scATAC-seq FASTQ to Count Matrix
1.0

Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial Pre-processing of 10X Single-Cell ATAC-seq Datasets, available in the GTN

Features

Thanks to...

Workflow Author(s): Pavankumar Videm

Tutorial Author(s): Pavankumar Videm

Tutorial Contributor(s): Cristóbal Gallardo, Pavankumar Videm, Björn Grüning, Helena Rasche, Mehmet Tekman, Wendi Bacon, Timon Schlegel

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Barcodes FASTQ (R2) Barcodes FASTQ (R2) n/a
  • File
Forward reads FASTQ (R1) Forward reads FASTQ (R1) n/a
  • File
Reverse reads FASTQ (R3) Reverse reads FASTQ (R3) n/a
  • File

Steps

ID Name Description
3 Sinto barcode toolshed.g2.bx.psu.edu/repos/iuc/sinto_barcode/sinto_barcode/0.9.0+galaxy1
4 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
5 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
6 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2
7 Sinto fragments toolshed.g2.bx.psu.edu/repos/iuc/sinto_fragments/sinto_fragments/0.9.0+galaxy1
8 bedtools SortBED toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy2
9 MACS2 callpeak toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0
10 Unique toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0
11 Build count matrix toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_build_matrix/episcanpy_build_matrix/0.3.2+galaxy1
12 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1
13 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1
14 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1
15 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:56 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:56

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