Query SDK fileType
 | Abbreviations Key | ||||
| AIFI | Allen Institute for Immunology | QC | quality control | ||
| FQ | fast queue | TEA-seq | transcripts, epitopes, and chromatin accessibility sequencin | ||
| fRNA | fixed RNA | TSS | transcription start site | ||
| GS | gating set | scATAC-seq | small cytoplasmic assays for transposase-accessible chromatin sequencing |
At a Glance
This document lists and describes all available result file types in the HISE SDK and explains how to retrieve file metadata. Python users can generate a current list of available fileTypes by calling hp.get_result_files().
Retrieve File Metadata
Each result file has associated metadata fields. To obtain file information, use get_file_descriptors(), along with the fileType parameter and a filter, as in the following examples. The string values you pass in, however, are not always clear.
| Python | hp.get_file_descriptors({‘fileType’:[‘atac-assembly-archr-arrow’]}) |
| R | getFileDescriptors(fileType=’atac-assembly-archr-arrow’) |
Query Available fileTypes
The following table lists all the result files you can query for.
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 |
Related Resources