File Definitions

File types

Several files are associated with different aspects of studies. Each section here describes a file, indicates their use, and provides an example. Depending on the wishes of the study owner, these files can be supplied and downloaded as a part of a study.

Primary sequencing files

Fastq.gz or Fastq.tar.gz

Visualization files

Cluster files
Metadata file
Expression file

Analysis files

Gene lists

Other files

Miscellaneous files

Checking files

Several of the file types below can be checked with the verify_portal_file.py script. The links below provide example commands of how to check each file individually. For the supported file types, the script can be called with all files for a study at once. If used in this manner the script will check each file individually and then make sure they among each other (eg. checking the consistency of cell names between all files). This is the best use of the script; an example of how to call the script with all files follows.

# To check the format of your file use the script verify_portal_file.py
# Requires python 3.x
python verify_portal_file.py --cluster-file cluster_1.txt cluster_2.txt --metadata-file metadata_example.txt --expression-files expression_example.txt --gene_list genes_1.txt gene_2.txt