scATAC-seq FASTQ to Count Matrix 1
Visit source
Download RO-CrateGalaxy workflow
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Barcodes FASTQ (R2) | Barcodes FASTQ (R2) | n/a |
|
| Forward reads FASTQ (R1) | Forward reads FASTQ (R1) | n/a |
|
| Reverse reads FASTQ (R3) | Reverse reads FASTQ (R3) | n/a |
|
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 (earliest) Created 22nd Apr 2024 at 11:19 by Helena Rasche
Added/updated 3 files
Open
masterbd85fb5
Creators and Submitter
Views: 232 Downloads: 70
Created: 22nd Apr 2024 at 11:19
Last updated: 22nd Apr 2024 at 11:19
TagsThis item has not yet been tagged.
AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service
Web page: Not specified
Space: General
Public web page: https://galaxy.training
