LabxDB seq

Schema

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.

Assign

Tools

With provided scripts sequencing data and their annotations can be imported and exported from sequencing center and external resources such as SRA.

Script	Function
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).

Scripts

Installation

These steps have to be done only the first time data is downloaded and imported.

Install LabxDB Python module including scripts.

Create folders

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

Tutorials

Tutorial	Script	Description
Tutorial 1	`import_seq`	How to import your high-throughput sequencing data in LabxDB seq? From downloading data from your sequencing center to annotate samples.
Tutorial 2	`export_sra`	How to export your high-throughput sequencing data to SRA? This greatly simplify export your own data to SRA at the time of publication.
Tutorial 3	`import_sra`	How to import publicly available high-throughput sequencing data from SRA?
Tutorial 4	`import_sra_id`	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.

NoteA working LabxDB seq database is required for this section. See the Installation section for help setup up your LabxDB seq database.

TipStart your own LabxDB in a virtual machine (Deploy). Check that your VirtualBox or QEMU instance works at http://127.0.0.1:8081. All links in these tutorials will use your virtual machine.