Hello, I am trying to do microRNA-seq for the first time. I am starting with the raw .fastq files for my samples. We were having some trouble establishing database access to miRBase, a reference library for known microRNAs. We were able to find a workaround with another pipeline for now, but we would prefer to use this one.
We have to edit the configuration file (code below) with credentials in order for our institution's high performance computational cluster (a Unix-based cluster) to have access to miRBase. It wants a host name, username, and password (miRBase is also open to the public, which further confuses me as to why it wants credentials). We were able to find this info for the UCSC database but nowhere could we find this info for miRBase. Also if we could get some guidance for how to use mySQL client in Unix to establish database connection, that would be nice. Any help would be appreciated. Thank you.
#This file stores information about databases to connect to.
#File format is <db_name> <host> <user> <password>
#Some examples: UCSC
#hg18 my_host my_user my_password
#hg19 my_host my_user my_password
#mm9 my_host my_user my_password
#Some examples: mirBase
#mirna_13_0 my_host my_user my_password (uses hg18 coordinates)
#mirna_15 my_host my_user my_password (mirbase 15 through 20 use GRCh37 coordinates)
#mirna_16 my_host my_user my_password
#mirna_19 my_host my_user my_password
#mirna_20 my_host my_user my_password
Link to the pipeline we are using: https://github.com/bcgsc/mirna
You can create a local mysql instance of the miRBase by downloading database_files from ftp site.
Check the
How can I access all the database files?section in FAQ .