Reminder: GCBridge is the tool that automatically transfers your NGS data from GeneCore to both emBASE and Galaxy
Tracking of data release notification emails : this allows us to know what data has been validated and what data is still waiting for transfer validation by its owner.
Demultiplexing of the data directly in your NGS data library this new version of GCB also comes with a new emBASE version that expects demultiplexed files (fastq or bam) to be stored in precise places of your group NGS data library (found on your file server). The GCB validation form now offers to demulitplex data (with the flexible Jemultiplexer ). Demultiplexed data is automatically saved in the right place of your NGS data library. This insures that we always know where the data is, will avoid data duplication and ease the submission of your data upon publication!
Reuse of samples and libraries from emBASE : emBASE always creates new samples/extracts/libraries using your GCB submission. Although this greatly eases the submission of your data, this was problematic in a number of situations and limits the accurate modeling of technical replicates. The GCB now offers you to reuse sample(s) or library(-ies) already stored in emBASE. GCB uses the sample name(s) you provide in the text box to find matching emBASE sample(s)/library(-ies). If multiple possibilities are found, you must select the correct one.
Other features : Automatic fetching of experiment prefix, better guessing of the organism, optional data forward to Galaxy
We also greatly improved the handling and processing of shared lanes (lane’s samples belong to multiple users) and multi-project lanes (lane’s samples belong to a unique user but different project):
- We now ask the lane owner (the user who first receives the notification email and therefore the first user to validate the GCB form) for the total number of samples found in the lane. This allows us to know when all samples have been submitted to the system (something we need to know to launch demultiplexing at the right time!).
- We now ask each submitter for the total number of his/her samples found in the lane. This allows us to know when a user has completed his submission in case of multi-project lane (and to prevent multiple submissions).
- No more need to manually email GBCS about the names of lane-mates, the lane owner now simply select all lane-mates in the GCB form, and the system emails them directly
Updated GCBridge documentation:a step-by-step how-to explaining how to fill in the new transfer form in details, with screenshots, is available here.