Workflow Type: Galaxy
Stable

Takes 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
  • File
Expected Cells #main/Expected Cells Approximately how many cells are expected in this sample?
  • int
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.
  • array containing
    • File
Reference Genome fasta #main/Reference Genome fasta n/a
  • File
Reference annotation #main/Reference annotation n/a
  • File
Sample #main/Sample Short, unique sample name
  • string

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
  • File
RNA STARSolo on input dataset(s): Alignments #main/RNA STARSolo on input dataset(s): Alignments n/a
  • File
Feature Statistic Summaries #main/RNA STARSolo on input dataset(s): Barcode/Feature Statistic Summaries n/a
  • File
RNA STARSolo on input dataset(s): Barcodes filtered #main/RNA STARSolo on input dataset(s): Barcodes filtered n/a
  • File
RNA STARSolo on input dataset(s): Genes filtered #main/RNA STARSolo on input dataset(s): Genes filtered n/a
  • File
RNA STARSolo on input dataset(s): Matrix Gene Counts filtered #main/RNA STARSolo on input dataset(s): Matrix Gene Counts filtered n/a
  • File
RNA STARSolo on input dataset(s): log #main/RNA STARSolo on input dataset(s): log n/a
  • File

Version History

main @ 7581788 (latest) Created 30th May 2024 at 06:47 by Sarah Williams

Updated workflow versions for anndata version conflict bugfix


Frozen main 7581788

main @ fe052c0 Created 12th Dec 2023 at 03:08 by Sarah Williams

updated star solo index size to limit RAM useage since galaxy migration


Frozen main fe052c0

main @ a95a4ee (earliest) Created 22nd Jun 2023 at 07:47 by Sarah Williams

counts matrix workflow doc, affiliations


Frozen main a95a4ee
help Creators and Submitter
Creators
  • Sarah Williams
  • Mike Thang
  • Valentine Murigneaux
Submitter
Citation
Williams, S., Thang, M., & Murigneaux, V. (2023). {scRNAseq on galaxy workflows}.
License
Activity

Views: 2297   Downloads: 194

Created: 22nd Jun 2023 at 07:47

Last updated: 30th May 2024 at 06:47

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Total size: 3.75 MB
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