Promoter Test: FENDRR

RNA Target promoters 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 FENDRR
Organism -organism mm9
Promoter length -pl 1000
Alpha level for rejection p value -a 0.05
Cut off value for filtering out the low counts of DBSs -ccf 20
Remove temporary files -rt False
Input file for RNA accecibility -ac False
Cut off value for RNA accecibility -accf 500
Output the BED files for DNA binding sites. -obed False
Show parallel and antiparallel bindings in the plot separately. -showpa False
Minimum length -l 15
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

See details

For more details please visit the RGT Website