Sample Ingestion
Last updated
Last updated
Panomics supports the ingestion of transcriptomics samples from local and remote sources. The ingestion process requires a Standard Compute runtime.
Sample ingestion is a straightforward, multi-step process.
We recommend users upload samples in a project. This makes tracking and metadata setting simpler.
In Panomics, the concept of file mode was introduced to distinguish between one file per dataset (gene by samples or cells) and one file per sample (output from Salmon quantification).
single
- each sample will be uploaded as an individual file
combined
- all samples are represented in a single file
Users can import samples from their local disks, AWS S3 or DNAnexus. For AWS and DNAnexus, an external API key must be configured.
Depending on the sample source, this step will differ.
Local disk - drop you files in the upload area.
AWS S3 - input the name of the S3 bucket, the prefix, and a regex to select only the files you intend to import.
DNAnexus - select the DNAnexus project and a regex to select only the files you intend to import.
Batch ID - auto-generated ID to help you identify the sample batch easily.
Organism - the organism of the sample donors.
Genome assembly (or gene model)
Gene column - the name of the column that refers to the gene ID or gene symbol. Supported IDs are Ensemble and Entrez. Applies to CSV file inputs.
Transformed counts - whether you are uploading normalized and log-transformed counts.
Strip prefix characters - whether you would like the platform to strip one or more characters from the beginning of the sample names. This is useful if your sample names are numeric only, but the output was generated in R, which adds an X.
First sample column index - for combined samples, indicate what column index represents the first sample (zero-based).
Panomics supports the ingestion of normalized intensities files that have been mapped to gene IDs or gene symbols. Only the combined
sample file mode is accepted.
Accepted formats: .txt, .csv, .tsv, .zip, .gz
Example file:
Panomics supports the ingestion of raw or normalized and log-transformed bulk RNA-seq samples. Both single
and combined
file modes are accepted.
Accepted formats: .txt, .csv, .tsv, .zip, .gz
For single cell or single nucleus RNA-seq samples only the single
file mode is currently supported.
Accepted formats: .txt, .csv, .tsv, .zip, .gz
Zip files can contain 3 files that follow this convention:
GSM5474339_AD5_barcodes.tsv.gz
GSM5474339_AD5_features.tsv.gz
GSM5474339_AD5_matrix.mtx.gz