3-3. Analysis
G: Group field
Analysis Metadata
1
Analysis type
G (Analysis)
This has drop-down menus that allow you to select from a controlled vocabulary. See the Analysis type from for details Note: If there are multiple files, you can compress them into a single file using tar (.tar or .tar.gz)
2
Processed file name
G (Analysis)
Exact name of the file containing the processed data
Note: The same processed file may be listed for multiple Samples
3
Processed method
G (Analysis)
Provide detailed of how processed data files were generated. Step may include: Base-calling software, version, parameters; Read alignment software, version, parameters; Data filtering steps; etc
4
Reference type
G (Reference)
If you select REFERENCE_ALIGNMENT in the Analysis type, enter the reference group information. This has drop-down menus that allow you to select from a controlled vocabulary. See the Reference type from for details
5
Reference assembly
G (Reference)
This is only if you are submitting a bam file aligned against a NCBI assembly. Please provide the assembly used during your alignment.
Example: GRCh37
6
Reference FASTA file
G (Reference)
Please provide the name of the custom assembly fasta file, including extension, used during alignment
Example: Mouse.fasta
Analysis type
1
ABUNDANCE_MEASUREMENT
tsv, csv, txt
2
REFERENCE_ALIGNMENT
bam, sam, cram
3
SEQUENCE_VARIATION
vcf, bcf, gvcf, bed, wig, bedgraph, maf
Reference type
1
RefSeq
If references are found in https://ftp.ncbi.nlm.nih.gov/sra/refseq/, please select Reference assembly and enter the references accession.version into reference name field
2
assembly
If references are not found in https://ftp.ncbi.nlm.nih.gov/sra/refseq/, please select Reference FASTA file and submit a reference file in multi-fasta format.
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