Promoter Test: FENDRR_FC

RNA Sig promoters All promoters Autobinding Parameters

Parameters

Description Arguments Value
RNA sequence name -rn FENDRR
Input RNA sequence file -r FENDRR.fasta
Input file for defferentially expression gene list -de fendrr_gene_list_fold_change.txt
Input BED file as promoters -bed False
Input BED file as backgrounds -bg False
Output directory -o ///home/joseph/rgt_test/TDF/TDF_examples/FENDRR_mm9/promoter_test/FENDRR_FC
Organism -organism mm9
filter_havana -filter_havana False
protein_coding -protein_coding False
known_only -known_only False
Promoter length -pl 1000
Alpha level for rejection p value -a 0.05
Cut off value for filtering out the DBD with low counts of triplexes -ccf 0.1
Remove temporary files -rt False
Output the BED files for DNA binding sites. -obed True
Show parallel and antiparallel bindings in the plot separately. -showpa False
Minimum length -l 20
Maximum error rate -e 20
Tolerated number of consecutive errors -c 2
Filtering repeats -fr off
Filtering mode -fm 0
Output format -of 1
Merge features -mf False



For more details please visit the RGT Website