LOCKED | Generating a single cell matrix using Alevin

Associated Tutorial

This workflows is part of the tutorial Generating a single cell matrix using Alevin, available in the GTN

Workflow Author(s): Julia Jakiela, Wendi Bacon

Tutorial Author(s): Wendi Bacon, Jonathan Manning

Tutorial Contributor(s): Helena Rasche, Julia Jakiela, Pavankumar Videm, Björn Grüning, Marisa Loach, Wendi Bacon, Teresa Müller, Saskia Hiltemann, Mehmet Tekman, Jonathan Manning, Beatriz Serrano-Solano, David López

Inputs

ID	Name	Description	Type
GTF file	#main/GTF file	You can find the file containing the gene information for your species here: http://www.ensembl.org/info/data/ftp/index.html/	File
Read 1 - containing cell barcode & UMI	#main/Read 1 - containing cell barcode & UMI	This should be a fast file containing the shorter read - i.e. the cell barcode and the unique molecular identifier	File
Read 2 - containing transcript	#main/Read 2 - containing transcript	This should be the read containing the transcript	File
Reference FASTA	#main/Reference FASTA	You can find this file for your species here: http://www.ensembl.org/info/data/ftp/index.html/	File

Steps

ID	Name	Description
4	Transcript-gene mapping	toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0
5	Gene Information Extraction	toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0
6	Alevin - no processing	toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy2
7	salmonKallistoMtxTo10x	toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6
8	Droplet rank plot - raw barcodes	toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2
9	Join two Datasets	join1
10	Cut	Cut1
11	DropletUtils Read10x	toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0
12	DropletUtils emptyDrops	toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0
13	SCEasy Converter	toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+galaxy2
14	Inspect AnnData	toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1
15	Manipulate AnnData	toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy1

Outputs

ID	Name	Description	Type
Annotated_Gene_Table	#main/Annotated_Gene_Table	n/a	File
Gene_Information	#main/Gene_Information	n/a	File
anndata	#main/anndata	n/a	File
barcodes_out	#main/barcodes_out	n/a	File
fasta_output	#main/fasta_output	n/a	File
fasta_output2	#main/fasta_output2	n/a	File
feature_annotation	#main/feature_annotation	n/a	File
genes_out	#main/genes_out	n/a	File
matrix_out	#main/matrix_out	n/a	File
out_file1	#main/out_file1	n/a	File
output_anndata	#main/output_anndata	n/a	File
output_rdata	#main/output_rdata	n/a	File
output_rds	#main/output_rds	n/a	File
plot_file-raw	#main/plot_file-raw	n/a	File
quants_mat_cols_txt_1	#main/quants_mat_cols_txt_1	n/a	File
quants_mat_mtx_1	#main/quants_mat_mtx_1	n/a	File
quants_mat_rows_txt_1	#main/quants_mat_rows_txt_1	n/a	File
raw_cb_frequency_txt	#main/raw_cb_frequency_txt	n/a	File
salmon_quant_log	#main/salmon_quant_log	n/a	File
var	#main/var	n/a	File