scATAC-seq FASTQ to Count Matrix
1.0

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Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial scATAC-seq FASTQ to Count Matrix, available in the GTN

Features

Thanks to...

Tutorial Author(s): Pavankumar Videm

Workflow Author(s): Pavankumar Videm

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1208?version=1

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 25th Jun 2024 at 11:10 by Helena Rasche

Added/updated 4 files


Open master f344309
help Creators and Submitter
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GTN Matrix
Tools
FastQC
BWA
BEDTools
MACS
epiScanpy
License
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Activity

Views: 987   Downloads: 297   Runs: 0

Created: 25th Jun 2024 at 11:10

Last updated: 25th Jun 2024 at 11:10

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