Preprocessing_Alevin
Created: 2022-05-16 10:06:03
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Workflow Components
Inputs (9)
| Name |
Description |
| reads |
F: 3'v2 CB +UMI
R: reads |
| gene_annotations.gtf |
|
| genome_transcipt.cdna.all.fa.gz |
|
| optional |
runtime parameter for tool Alevin |
| optional |
runtime parameter for tool Alevin |
| optional |
runtime parameter for tool Alevin |
| tenx_format |
runtime parameter for tool DropletUtils |
| tenx_format |
runtime parameter for tool DropletUtils |
| tenx_format |
runtime parameter for tool DropletUtils |
Steps (10)
| Name |
Tool |
Description |
| Input dataset collection |
None |
|
| Input dataset |
None |
|
| Input dataset |
None |
|
| Unzip collection |
__UNZIP_COLLECTION__ |
|
| GTF2GeneList |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0 |
|
| Alevin |
toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0 |
|
| salmonKallistoMtxTo10x |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy5 |
|
| DropletUtils |
toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 |
|
| DropletUtils |
toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 |
|
| DropletUtils |
toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 |
|
Outputs (35)
| Name |
Type |
| forward |
input |
| reverse |
input |
| feature_annotation |
tsv |
| fasta_output |
fasta.gz |
| quants_mat_mtx |
mtx |
| raw_cb_frequency_txt |
txt |
| quants_mat_cols_txt |
txt |
| quants_mat_rows_txt |
txt |
| quants_tier_mat |
mtx |
| alevin_log |
txt |
| featureDump_txt |
txt |
| whitelist_txt |
txt |
| alevinmeta_info_json |
json |
| ambig_info_tsv |
tsv |
| meta_info_json |
json |
| expected_bias |
txt |
| observed_bias |
txt |
| observed_bias_3p |
txt |
| flenDist_txt |
txt |
| salmon_quant_log |
txt |
| cmd_info.json |
json |
| genes_out |
tabular |
| barcodes_out |
tabular |
| matrix_out |
mtx |
| fileout_tsv |
tsv |
| plot |
png |
| table |
tsv |
| fileout_h5 |
h5 |
| plot |
png |
| table |
tsv |
| barcodes_out |
tsv |
| genes_out |
tsv |
| matrix_out |
mtx |
| plot |
png |
| table |
tsv |
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