T-Gene: Prediction of Target Genes Options: -annotation-file-name annotation file name -transcript-types types of transcript to use from annotation file -max-link-distances comma-separated list of maximum distances between an RE and its target -max-pvalue maximum p-value for including non-CT, non-CL links in output -tissues comma-separated list (no spaces) of tissue names -histone-root histone root directory -histones comma-separated list (no spaces) of histone names -rna-source type of RNA expression data you are providing -expression-root expression root directory -use-gene-ids use the 'gene_id' field rather than 'transcript_id' field to associate expression file and annotation file entries; -lecat low expression correlation adjustment threshold; default: 0 -no-closest-locus don't include closest locus for all targets unless constraints are satisfied -no-closest-tss don't include closest TSS (target transcript) for all loci unless constraints are satisfied Files present in the server tgene databases can be specified by appending 'db/' to the file name. ]]> use-gene-ids -use-gene-ids use the 'gene_id' field rather than 'transcript_id' field to associate expression file and annotation file entries false inc-closest-locus -inc-closet-locus include closest locus for all targets false inc-closest-tss -inc-closet-tss include closest TSS (target) for all loci false tissues -tissues STRING comma-separated list (no spaces) of tissue names histone-root -histone-root STRING histone root directory histones -histones STRING comma-separated list (no spaces) of histone names max-link-distances -max-link-distances STRING comma-separated list of maximum distances between an RE and its target expression-root -expression-root STRING expression root directory expression-file-type -expression-file-type STRING file type of expression files annotation-file-name -annotation-file-name STRING annotation file name annotation-type -annotation-type STRING type of annotation [Gencode|RefSeq] transcript-types -transcript-types STRING types of transcript to use from annotation file min-feature-count -min-feature-count INT only consider links where there is both histone and expression data for at least this many tissues min-max-expression -min-max-expression INT maximum expression of a target must be at least this large for the target to be included in the map max-html-score -max-html-score FLOAT only include links with this score or better in the HTML desc -desc STRING plain text description of the job locus_file FILE INPUT true Upload Loci in BED format rna_source STRING true the type of RNA expression data from the list: LongPap LongPapMouse LongPam Short Cage @SERVICE_DIR@/tgene_webservice @drmaa_queue@ false