The app “Retrieve-Brassica-Phenotypes” imports standardised Brassica trait data from the Brassica Information Portal (BIP) into CyVerse, so that the user can subsequently integrate this data into genotype-phenotype association analysis worflows.
Inputs are the trial name as it is registered in the BIP, as well as the BIP-API-key. You need to have a BIP account to retrieve your API-key. It is free to sign up and you can use your ORCiD for it. Please click renew your BIP-API-key in the BIP website after you downloaded data.
The main output file will be a .csv-file with accession identifiers, SRA-identifiers and the trait measurements of the trial. Sequence IDs get passed on into a Seq_names.txt file for further queries. It also creates a Sequence_IDs_log.txt, where the user can see whether some accessions did not have any or multiple Sequence IDs.
For more information on the app, please see the documentation.
Any feedback, praise or questions? contact us on email@example.com or tweet to us on @BrassicaP