Step | Annotation |
---|---|
Step 1: Input dataset
select at runtime
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|
Step 2: Input dataset
select at runtime
|
|
Step 3: Input dataset
select at runtime
|
|
Step 4: Input dataset
select at runtime
|
|
Step 5: GTF2GeneList
Output dataset 'output' from step 1
gene
gene_id
True
gene_id,gene_name,mito
True
True
mt,mitochondrion_genome,mito,m,chrM,chrMt
mt_trna,mt_rrna,mt_trna_pseudogene
False
|
|
Step 6: GTF2GeneList
Output dataset 'output' from step 1
transcript
transcript_id
True
transcript_id,gene_id
True
False
True
Output dataset 'output' from step 3
transcript_id
|
|
Step 7: Alevin
Use one from the history
Salmon index:
Output dataset 'fasta_output' from step 6
31
False
Paired-end
Output dataset 'output' from step 4
Output dataset 'output' from step 2
Mates are oriented toward each other (I = inward)
read comes from the reverse strand (SR)
DropSeq Single Cell protocol
Output dataset 'feature_annotation' from step 6
True
Optional commands:
select at runtime
False
select at runtime
select at runtime
False
True
False
True
Not available.
Not available.
Not available.
Not available.
1.0
Not available.
Not available.
3
|
|
Step 8: Alevin
Use one from the history
Salmon index:
Output dataset 'fasta_output' from step 6
31
False
Paired-end
Output dataset 'output' from step 4
Output dataset 'output' from step 2
Mates are oriented toward each other (I = inward)
read comes from the reverse strand (SR)
DropSeq Single Cell protocol
Output dataset 'feature_annotation' from step 6
True
Optional commands:
select at runtime
False
select at runtime
select at runtime
False
True
False
True
Not available.
Not available.
Not available.
Not available.
Not available.
Not available.
Not available.
Not available.
|
|
Step 9: salmonKallistoMtxTo10x
Output dataset 'quants_mat.mtx' from step 7
Output dataset 'quants_mat_cols.txt' from step 7
Output dataset 'quants_mat_rows.txt' from step 7
Empty.
|
|
Step 10: Droplet barcode rank plot
False
Output dataset 'raw_cb_frequency.txt' from step 8
Barcode rank plot (raw barcode frequencies)
50
1.5
|
|
Step 11: Droplet barcode rank plot
True
Output dataset 'quants_mat.mtx' from step 8
True
Barcode rank plot (Alevin-processed)
50
1.5
|
|
Step 12: Join two Datasets
Output dataset 'genes_out' from step 9
1
Output dataset 'feature_annotation' from step 5
1
Yes
Yes
No
No
|
|
Step 13: Cut
c1,c4,c5
Tab
Output dataset 'out_file1' from step 12
|
|
Step 14: DropletUtils Read10x
Output dataset 'matrix_out' from step 9
Output dataset 'out_file1' from step 13
Output dataset 'barcodes_out' from step 9
False
|
|
Step 15: DropletUtils emptyDrops
Output dataset 'output_rds' from step 14
5
1000
0.01
False
Not available.
Not available.
True
|
|
Step 16: DropletUtils emptyDrops
Output dataset 'output_rds' from step 14
100
1000
0.01
False
Not available.
Not available.
True
|
|
Step 17: SCEasy convert
SingleCellExperiment to AnnData
Output dataset 'output_rdata' from step 15
counts
|
wendi.bacon.training
All published workflows
Published workflows by wendi.bacon.training