The eqmr-prbannot program takes a database created by the eqmr-db as input and outputs the probe annotations. It can also be used to generate other useful annotation files for subsequent analyses with eqtnminer.
|--meta-exon||Output meta-exon probe annotation|
|--gene-model||Output .txtab files corresponding to the gene model for each probe|
|--exon-model||Output .txtab files corresponding to the exon model for each probe|
|-d||--data||a previously created database (binary file with the .db extension)|
|-o||--output||The output directory for --gene-model and --exon-model (otherwise output is generated on stdout)|
First, after the creation of the database file, let's get the probe annotation file as follows:
$ eqmr-prbannot -d eqmr.db 1>probe_annot.txt
Then, we can get the so-called "gene model" for each probe, i.e. the list of transcripts interrogated by each probe. The output format is the same than the gene annotation file provided as input for eqmr-db.
$ eqmr-prbannot -d eqmr.db -o probe_gene_model
this will create the folder probe_gene_model that will contain as many files as the number of chromosomes and each file is formated as the input .txtab format, with the difference that the probe identifier will be reported as the first column.