LabxDB seq is composed of 3 levels: project, sample, replicate and run. Each level is stored in a table. Columns within each table are described here.
With provided scripts sequencing data and their annotations can be imported and exported from sequencing center and external resources such as SRA.
|import_seq||Import your sequencing data from your local sequencing center.|
|export_sra||Export your sequencing data annotations to SRA. Prepare tabulated files for SRA import with your annotations.|
|export_sra_fastq||Export your sequencing data to SRA. Prepare FASTQ file(s). Helper script of export_sra.|
|import_sra_id||Import SRA IDs to your sequencing data annotations, i.e. import SRRxxx, SRPxxx etc to your database.|
|import_sra||Import SRA data (FASTQ and annotations).|
These steps have to be done only the first time data is downloaded and imported.
Install LabxDB Python module including scripts.
Choose a root folder for your sequencing data, here this will be
/data/seq. Then create the following sub-folders:
mkdir /data mkdir /data/seq mkdir /data/seq/raw # For RAW sequencing data mkdir /data/seq/by_run # For symbolic links to sequencing runs mkdir /data/seq/prepared # For imported/reformated sequencing data
||How to import your high-throughput sequencing data in LabxDB seq? From downloading data from your sequencing center to annotate samples.|
||How to export your high-throughput sequencing data to SRA? This greatly simplify export your own data to SRA at the time of publication.|
||How to import publicly available high-throughput sequencing data from SRA?|
||How to import the SRA attributed by SRA to your high-throughput sequencing data after import to SRA? Importing SRA IDs to your database allows you to keep track of exported (i.e. published) or not samples.|