scRNAseq: Count and Load with starSOLO
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Run on GalaxyTakes fastqs and reference data, to produce a single cell counts matrix into and save in annData format - adding a column called sample with the sample name.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Barcode Whitelist file | #main/Barcode Whitelist file | Obtain from kit supplier e.g. 10X |
|
| Expected Cells | #main/Expected Cells | Approximately how many cells are expected in this sample? |
|
| Paired Fastqs for one sample | #main/Paired Fastqs for one sample | Typically the Forward reads are labelled _R1, barcodes. R2 is Reverse, mRNA sequences. List should contain seq for one biological sample only. |
|
| Reference Genome fasta | #main/Reference Genome fasta | n/a |
|
| Reference annotation | #main/Reference annotation | n/a |
|
| Sample | #main/Sample | Short, unique sample name |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | Unzip collection | __UNZIP_COLLECTION__ |
| 7 | Forward/R1/barcode Fastq Concat | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 8 | Reverse/R2/mRNA Fastq concat | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 9 | RNA STARSolo | toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0 |
| 10 | Scanpy Read10x | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.9.3+galaxy0 |
| 11 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 12 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1 |
| 13 | Text transformation | This step replaces the first line with a header. Because the annotated data matrix also had a header, this works. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
| 14 | Loaded Anndata with Sample name | AnnData object with supplied sample id. toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| AnnData Loaded | #main/AnnData Loaded | n/a |
|
| RNA STARSolo on input dataset(s): Alignments | #main/RNA STARSolo on input dataset(s): Alignments | n/a |
|
| Feature Statistic Summaries | #main/RNA STARSolo on input dataset(s): Barcode/Feature Statistic Summaries | n/a |
|
| RNA STARSolo on input dataset(s): Barcodes filtered | #main/RNA STARSolo on input dataset(s): Barcodes filtered | n/a |
|
| RNA STARSolo on input dataset(s): Genes filtered | #main/RNA STARSolo on input dataset(s): Genes filtered | n/a |
|
| RNA STARSolo on input dataset(s): Matrix Gene Counts filtered | #main/RNA STARSolo on input dataset(s): Matrix Gene Counts filtered | n/a |
|
| RNA STARSolo on input dataset(s): log | #main/RNA STARSolo on input dataset(s): log | n/a |
|
Version History
main @ 7581788 (latest) Created 30th May 2024 at 06:47 by Sarah Williams
Updated workflow versions for anndata version conflict bugfix
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main7581788
main @ fe052c0 Created 12th Dec 2023 at 03:08 by Sarah Williams
updated star solo index size to limit RAM useage since galaxy migration
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main
fe052c0
main @ a95a4ee (earliest) Created 22nd Jun 2023 at 07:47 by Sarah Williams
counts matrix workflow doc, affiliations
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a95a4ee
Creators and SubmitterViews: 3999 Downloads: 383 Runs: 0
Created: 22nd Jun 2023 at 07:47
Last updated: 30th May 2024 at 06:47
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scRNAseq processing...
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Teams: QCIF Bioinformatics
Organizations: QCIF
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia
Web page: https://www.biocommons.org.au/
Working closely with researchers, the QCIF Bioinformatics team apply data management, processing, integration, analysis and visualisation techniques to maximise the potential value of biological and clinical data sets. QCIF Bioinformatics is a partner in the Australian BioCommons.
Space: Australian BioCommons
Public web page: https://www.qcif.edu.au/
This collection houses some scanpy-based scRNAseq workflows on galaxy Australia.
The aim of these workflows is to handle the routine ‘boring’ part of single cell RNAseq data processing. It will produces an ‘AnnData’ object, which can then be used as a base for downstream analysis – either within galaxy or outside of it. AnnData is a standard format used by the ‘scanpy’ python package.
These workflows represent just one way of processing data for a ‘typical’ scRNAseq experiment – there are many ...
