Data Transfer From Partek Flow

Partek Flow project can't be directly transfer to Connected Multiomics study, user can download certain format of files from Partek Flow project and upload to Connected Multiomics.

Connected Multiomics doesn't support FASTQ or BAM file format, it takes Illumina secondary analysis output files, or sample by feature matrix file in text format.

Below are the instructions on how to download data from Partek Flow to local computer on different assays.

Bulk mRNA and miRNA-Seq

In Partek Flow, bulk RNA-Seq (mRNA and other small RNA) data, export the data node contains count matrix, raw counts, or normalized count. E.g. bulk RNA analysis generate gene counts/transcript counts after quantification, the data node contains raw counts matrix at gene/transcript level:

Click on a data node e.g. Gene counts data node, choose Download data at the bottom of the pop-up menu, choose export option:

Choose either features on column (which means samples are on rows) or features on rows (samples are on columns). Annotation information will be exported if that checkbox is selected, only the row annotation will be exported:

• When choose features on columns, only sample annotation can be exported.

• When choose Features on rows, only feature annotation can be exported.

Downloaded data is in a .zip file, decompress the file to retrieve the tab delimited text file in .txt format.

scRNA-Seq

Single-cell RNA-Seq data can be exported as count matrix, it is similar as bulk RNA data export above. When choose Features on column options, all the sample annotation and cell annotation store on the Metadata tab will be included in the text file if Annotation checkbox is selected. However, export data in h5ad format is recommended because you have options to include more information on cells.

Select either the raw count matrix data node or normalized count data node, choose Export to h5ad files under Conversion section on the pop-up menu. This option is only available when you select a data node contains cell by feature count matrix.

In the dialog, you will have option to select data node like PCA, UMAP, t-SNE and Graph-based cluster, K-means-cluster if they are in your analysis pipeline. If you have multiple those results in your pipeline, you can only choose one of them.

After click Finish, an H5ad file data node will be generated. Download it and import it to Connected Multiomics.

Bulk ATAC/ChIP-Seq

Connected Multiomics accepts region counts as input for ATAC/ChIP-Seq data, which is a matrix of sample by region matrix. This information is stored in the output of Quantify to region task. In the matrix, the feature ID contains the genomic location of the region, represented by chromosome, start, stop.

The download option is similar to Bulk RNA-Seq.

DNA-Seq

Variant or annotated variant data nodes can be downloaded as VCF file to be imported into Connected Multiomics.

Click on a variant data node, choose Download data from the pop-up menu

Choose to export vcf one sample per file or merge all the samples into one vcf option and click Download.