Query SDK fileType
 | Abbreviations Key |
| AIFI | Allen Institute for Immunology |
| FQ | fast queue |
| fRNA | fixed RNA |
| GS | gating set |
| QC | quality control |
| scATAC-seq | small cytoplasmic assays for transposase-accessible chromatin sequencing |
| TEA-seq | transcripts, epitopes, and chromatin accessibility sequencing |
| TSS | transcription start site |
Each result file has associated metadata fields. In order to obtain file information we use getFileDescriptors() function along with fileType parameter and a filter. The string values you pass in to this method is not always clear, so this page contains information on all the result files you can query for.
Example:
R: getFileDesctipors(fileType=’atac-assembly-archr-arrow’)
Python: hp.get_file_descriptors({‘fileType’:[‘atac-assembly-archr-arrow’]})
Filetype | Description | Group | Account |
atac-assembly-archr-arrow | scATAC-seq .arrow file for use with the ArchR framework | ATAC-seq | All |
atac-assembly-filtered-fragments-tsv-gz | scATAC-seq fragments.tsv.gz file for use with other analysis frameworks | ATAC-seq | All |
atac-assembly-read-counts-per-windows-h5 | scATAC-seq fragment counts per genomic 5kb window | ATAC-seq | All |
atac-assembly-read-counts-gene-bodies-h5 | scATAC-seq fragment counts per gene body | ATAC-seq | All |
atac-assembly-read-counts-per-region-h5 | scATAC-seq fragment counts per TSS (+/-2kb) | ATAC-seq | All |
atac-archr-label-results | ATAC archer label results | ATAC-seq | All |
cellranger-atac-possorted_genome | Cellranger atac possorted genome | ATAC-seq | All |
Olink | Olink data matrix (cross-project) | Olink proteomics | All |
frna-labled-h5 | Labeled H5 Files | Fixed RNA | All |
frna-qc-report | fRNA QC report | Fixed RNA | All |
Fixed RNA FQ | valign="top"
Fixed RNA fast queue | Fixed RNA | AIFI Internal |
Fixed RNA-seq Manifest | Fixed RNA Seq Manigest file | Fixed RNA | AIFI Internal |
scRNA seq FQ file | scRNA-seq FQ | scRNA-seq | All |
scRNA-seq manifest | scRNA-seq Manifest | scRNA-seq | All |
scRNA cellhashing main qc report | scRNA-seq-CellHashing-Main-QC-report | scRNA-seq | All |
Labeled scRNA-seq .h5 dataset | “scRNA-seq-labeled” | scRNA-seq | All |
Cytometry - live logical transform csv | FlowCytometry-decoration-report-csv | Cytometry | All |
Flow QC report HTML | FlowCytometry-decoration-report-html | Cytometry | All |
FlowCytometry-labeled-expr-csv | Cyanno - Labeled Expr CSV | Cytometry | All |
FlowCytometry-prediction-report | Pipeline result report file | Cytometry | All |
FlowCytometry-summary-frequency-stats | Cyanno - summary frequency stats csv | Cytometry | All |
FlowCytometry-supervised-comp | Cytometry - supervised gating compensation | Cytometry | All |
FlowCytometry-supervised-gating-set-gs | Cytometry - Supervised Gating Set GS | Cytometry | All |
FlowCytometry-supervised-gating-set-h5 | Cytometry - Supervised Gating Set H5 | Cytometry | All |
FlowCytometry-supervised-gating-set-pb | Cytometry - Supervised Gating Set PB | Cytometry | All |
FlowCytometry-supervised-mfis | Cytometry - Supervised Gating MFI | Cytometry | All |
FlowCytometry-supervised-stats | Cytometry - Supervised Gating Population Counts | Cytometry | All |
adt-batch-summary-report | Pipeline result report file | TEA-seq | All |
adt-tea-seq-well-report | TEA-seq adt well report | TEA-seq | All |
tea-main-batch-summary-report | Pipeline result report file | TEA-seq | All |
spatial-analysis-metric-view | Spatial analysis metrics view | Spatial | All |
spatial-analysis-qx-report | Pipeline result report file | Spatial | All |
Detected Transcripts | Detected Transcripts | Vizgen | AIFI Internal |
Vizgen Image | Vizgen Image | Vizgen | AIFI Internal |
Vizgen Manifest | Vizgen Manifest | Vizgen | AIFI Internal |
spatial-segment-cell-boundaries-parquet | Vizgen | AIFI Internal | |
spatial-segment-cell-bygene | Vizgen | AIFI Internal | |
spatial-segment-detected-transcripts | Vizgen | AIFI internal |
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