Pre-processing with Alevin - Part 2

StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset
select at runtime
Step 4: Input dataset
select at runtime
Step 5: Input dataset
select at runtime
Step 6: Input dataset
select at runtime
Step 7: Input dataset
select at runtime
Step 8: EBI SCXA Data Retrieval
E-MTAB-6945
Raw filtered counts
Step 9: Manipulate AnnData
Output dataset 'output' from step 7
Concatenate along the observations axis
Output dataset 'output' from step 1,Output dataset 'output' from step 3,Output dataset 'output' from step 4,Output dataset 'output' from step 5,Output dataset 'output' from step 6,Output dataset 'output' from step 2
Intersection of variables
batch
-
Step 10: Scanpy Read10x
Output dataset 'matrix_mtx' from step 8
Output dataset 'genes_tsv' from step 8
Output dataset 'barcode_tsv' from step 8
Output dataset 'design_tsv' from step 8
select at runtime
AnnData format
Gene ID
Step 11: Inspect AnnData
Output dataset 'anndata' from step 9
Key-indexed observations annotation (obs)
Step 12: Inspect AnnData
Output dataset 'anndata' from step 9
Key-indexed annotation of variables/features (var)
Step 13: Inspect AnnData
Output dataset 'anndata' from step 9
General information about the object
Step 14: Replace Text
Output dataset 'obs' from step 11
Replacements
Replacement 1
9
0|1|3|4|5|6
male
Replacement 2
9
2
female
Replacement 3
9
batch
sex
Step 15: Replace Text
Output dataset 'obs' from step 11
Replacements
Replacement 1
9
0|3|4|5
wildtype
Replacement 2
9
1|2|6
knockout
Replacement 3
9
batch
genotype
Step 16: Cut
c9
Tab
Output dataset 'outfile' from step 14
Step 17: Cut
c9
Tab
Output dataset 'outfile' from step 15
Step 18: Paste
Output dataset 'out_file1' from step 17
Output dataset 'out_file1' from step 16
Tab
Step 19: Manipulate AnnData
Output dataset 'anndata' from step 9
Add new annotation(s) for observations or variables
Observations (obs)
Output dataset 'out_file1' from step 18
Step 20: Manipulate AnnData
Output dataset 'anndata' from step 19
Rename categories of annotation
batch
N701,N702,N703,N704,N705,N706,N707
Step 21: AnnData Operations
Output dataset 'anndata' from step 20
AnnData format
False
Change field names in AnnData observations
NA.
Flag genes that start with these names
Flag genes that start with these names 1
True
mito
50
False
False
False
False