Generating a single cell matrix using Alevin

This workflow generates 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

Tutorial Author(s): Wendi Bacon, Jonathan Manning

Tutorial Contributor(s): Helena Rasche, Julia Jakiela

Workflow Author(s): Julia Jakiela, Wendi Bacon

Inputs

ID	Name	Description	Type
GTF file	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	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	Read 2 - containing transcript	This should be the read containing the transcript	File
Reference FASTA	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	GTF2GeneList	toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0
5	Transcript-gene mapping	toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0
6	Alevin Processed	toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0
7	Alevin - no processing	toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0
8	Droplet rank plot - raw barcodes	toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2
9	Droplet rank plot - Alevin barcodes	toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2
10	salmonKallistoMtxTo10x	toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6
11	Join two Datasets	join1
12	Cut	Cut1
13	DropletUtils Read10x	toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0
14	DropletUtils emptyDrops	toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0
15	SCEasy Converter	toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+galaxy2

Outputs

ID	Name	Description	Type
fasta_output	fasta_output	n/a	File
feature_annotation	feature_annotation	n/a	File
raw_cb_frequency_txt	raw_cb_frequency_txt	n/a	File
salmon_quant_log	salmon_quant_log	n/a	File
quants_mat_mtx	quants_mat_mtx	n/a	File
quants_mat_cols_txt	quants_mat_cols_txt	n/a	File
quants_mat_rows_txt	quants_mat_rows_txt	n/a	File
quants_mat_rows_txt_1	quants_mat_rows_txt_1	n/a	File
quants_mat_mtx_1	quants_mat_mtx_1	n/a	File
quants_mat_cols_txt_1	quants_mat_cols_txt_1	n/a	File