Conversion

When download single cell or spatial matrix data, because of the size of the data, Connected Multiomics needs to first convert the files in the data node to a different file format, then transfer to your local computer.

Click on a count data node or normalized count data node, there are two options in conversion section:

Export to h5ad files:

This option allows to export cell by feature matrix with other annotation of the cells, like PCA, UMAP, t-SNE coordinates of the cells and cluster annotation if they are performed in the analysis:

Click on each of the Select data node to choose the node in the analysis pipeline, you can select only one of the same annotation type if performed multiple times of the same task, e.g. you perform graph-based cluster task multiple times with different parameter, you can only choose one to export.

After click Finish, you will see a new data node generated, click on the node, you can download the file:

Export matrix

This option allows you to export a text file of the full matrix or sparse matrix in 10X CellRanger .h5 format:

When export the full matrix in .txt file, you can choose features on columns or rows. You can choose to export annotation and/counts in the matrix by check the boxes in the Include content section. Only one level of annotation can be exported depends who is on row in the text file: if you choose features on columns option, cells will be on rows, then only cell annotation will be exported; if you choose features on rows, then only feature annotation will be exported.

If you have multiple samples in the analysis, check Combine samples will generate one text file with all the cells from all the samples. If you don't check the box, you will generate one text file for each sample individually.