How to Submit Other Analyses

Introduction

Any secondary analyses you wish to submit to ENA that are not Assemblies or Annotated Sequences need to be submitted programmatically.

All submissions to ENA must be part of an ENA Study. This gives context to the data being submitted and controls the release date of the associated data.

Other submission objects may also need submitting before you can submit your secondary analyses depending on the analysis type. E.g. read alignments require a raw read submission as well as a Study.

The analysis XML format is defined by SRA.analysis.xsd XML Schema.

Please note some analysis types require certain object relations so please read the individual submission guides for more detail on what needs submitting for each analysis type and please register all required objects before beginning your analysis submission.

How to register/submit other datasets to ENA:

• Register a study

• Register samples

• Submit raw reads

Submission Options

All analyses require programmatic submission.

For an overview of how to submit programmatically, please see the documentation on Programmatic Submissions.

• Submitting Read Alignments
• Submitting Sequence Annotations
• Submitting PacBio Methylation Data
• Submitting BioNano Maps
• Submitting Taxonomic Reference Sets

Analysis File Groups

For each analysis type, only specified pre-defined groups of files are allowed in a submission. The allowed file group(s) for each analysis type are enumerated in the below table. There may be multiple allowed groups for each analysis type, and the amount of files may be a range rather than a single integer.

Using This Table: Having identified the analysis type you wish to submit, find it in the table and consider all file groups available for it. A single file group will occupy multiple lines if it includes multiple types of file. Not all file types will be mandatory for a file group, which will be indicated by the ‘Allowed Quantity’ column showing that 0 is an acceptable quantity of files for a given type.

Analysis Type	File Group Name	File Format	Allowed Quantity
Genome Map	Bionano Native	BIONANO_NATIVE	1+
Reference Alignment	Single BAM	BAM	1
	Single CRAM	CRAM	1
PacBio Methylation	Sequence Methylation	GFF	1
Sequence Annotation	Sequence Methylation	TAB	0-2
	Single TAB	TAB	1
	Single FASTA	FASTA	1
	Single BED	BED	1
	Single GFF	GFF	1
Taxonomic Reference Set	Taxonomic Reference Set	FASTA	1
	Taxonomic Reference Set	TAB	1