CS1_Generating a single cell matrix using Alevin

ID	Name	Description	Type
Mus_musculus.GRCm38.100.gtf.gz	#main/Mus_musculus.GRCm38.100.gtf.gz	You can find the file containing the gene information for your species here: http://www.ensembl.org/info/data/ftp/index.html/	File
Mus_musculus.GRCm38.cdna.all.fa	#main/Mus_musculus.GRCm38.cdna.all.fa	You can find this file 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

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	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/1.5.1+galaxy0
7	Alevin - no processing	toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0
8	Droplet rank plot - Alevin barcodes	toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2
9	Droplet rank plot - raw 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	Annotated Gene Table	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	N701-400k-AnnData	toolshed.g2.bx.psu.edu/repos/ebi-gxa/sceasy_convert/sceasy_convert/0.0.5+galaxy1

ID	Name	Description	Type
N701-400k-AnnData	#main/N701-400k-AnnData	n/a	File
Stringent-Object	#main/Stringent-Object	n/a	File
_anonymous_output_1	#main/_anonymous_output_1	n/a	File
_anonymous_output_10	#main/_anonymous_output_10	n/a	File
_anonymous_output_11	#main/_anonymous_output_11	n/a	File
_anonymous_output_12	#main/_anonymous_output_12	n/a	File
_anonymous_output_13	#main/_anonymous_output_13	n/a	File
_anonymous_output_14	#main/_anonymous_output_14	n/a	File
_anonymous_output_15	#main/_anonymous_output_15	n/a	File
_anonymous_output_16	#main/_anonymous_output_16	n/a	File
_anonymous_output_17	#main/_anonymous_output_17	n/a	File
_anonymous_output_18	#main/_anonymous_output_18	n/a	File
_anonymous_output_19	#main/_anonymous_output_19	n/a	File
_anonymous_output_2	#main/_anonymous_output_2	n/a	File
_anonymous_output_20	#main/_anonymous_output_20	n/a	File
_anonymous_output_3	#main/_anonymous_output_3	n/a	File
_anonymous_output_4	#main/_anonymous_output_4	n/a	File
_anonymous_output_5	#main/_anonymous_output_5	n/a	File
_anonymous_output_6	#main/_anonymous_output_6	n/a	File
_anonymous_output_7	#main/_anonymous_output_7	n/a	File
_anonymous_output_8	#main/_anonymous_output_8	n/a	File
_anonymous_output_9	#main/_anonymous_output_9	n/a	File

CS1_Generating a single cell matrix using Alevin
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