Experiment and Run

The sequencing reads can be submitted in the STOmics submission portal.

The template consists of four parts:

  1. Metadata, describing associated tissue section, spatial slides, library and sequencing information.

    Metadata is required and cannot be left blank.
    tissue section alias: multiple values ​​are supported, separated by commas.
    spatial slide: multiple values ​​are supported, separated by commas.
    library name is unique for each library.
    Fixed value or drop-down options have been given for some fields.

  2. Fastq data files

.fastq.gz, .fastq.bz2, .fq.gz, .fq.bz2 are accept for fastq format data files.

MD5 values for these files should be filled in the template.

The fastq format is the most commonly submitted.

  1. Aligned data files

The file name needs to be suffixed with .bam. The md5 value is also required.

  1. Referenece data files

They are not mandatory. Sequence and annotation are supported if available.

There are two ways to submit them.

  • The reference accession in the public repository. For example, GRCh38.p14, NCBI Homo sapiens Annotation Release 108, GENCODE 40.

  • Custom data file and its md5 value.

.fa, .fasta, .fna, .fna.gz, .fa.gz, .fasta.gz, .fna.bz2, .fa.bz2, .fasta.bz2 are accept for sequence submission. .gff.gz, .gff3.gz, .gtf.gz are accept for annotation data submission.

For more detailed explanation for the fields, please refer to the standard below:

Important

  • The number of rows in the template cannot be greater than 800, and the template file cannot be greater than 10MB.

  • All file names and MD5 values ​​cannot be repeated in the template, expect reference data.

  • The data files that have been submitted cannot be submitted again, judged according to the MD5 value.

  • Both fastq data and aligned data must be submitted at least one.

  • If need to modify, the assigned accession numbers can not be modified.