Hi,

For running [ActivedriverWGS](https://github.com/reimandlab/ActiveDriverWGS) software I will need coding or non coding parts of genome in BED12 format. I have found coding part of genome (in txt format though). But I don't know how to find non coding part of genome (BED12 format) also Transcription factor binding  in BED4 format. I have contacted the developer but no response. Any suggestion please?




Sorry, finally I got what I want

I actually need enhancers, promoters, or other regulatory elements of human genome to find cancer driver genes placed in these regions

People says by 

     awk '$3=="transcript" && 
         $20!="\"protein_coding\";" &&
         $20!="\"translated_processed_pseudogene\";"' gencode.gtf

Will return non-coding parts of regions

like

    awk '$3=="transcript" && $20!="\"protein_coding\";"{print $20}' gencode.gtf  | sort | uniq -c | sort -nk1
          1 "translated_processed_pseudogene";
          2 "Mt_rRNA";
          3 "IG_J_pseudogene";
          3 "TR_D_gene";
          4 "TR_J_pseudogene";
          5 "TR_C_gene";
         10 "IG_C_pseudogene";
         18 "IG_C_gene";
         18 "IG_J_gene";
         22 "Mt_tRNA";
         25 "3prime_overlapping_ncrna";
         27 "TR_V_pseudogene";
         37 "IG_D_gene";
         58 "non_stop_decay";
         59 "polymorphic_pseudogene";
         74 "TR_J_gene";
         97 "TR_V_gene";
        144 "IG_V_gene";
        182 "unitary_pseudogene";
        196 "IG_V_pseudogene";
        330 "sense_overlapping";
        387 "pseudogene";
        442 "transcribed_processed_pseudogene";
        531 "rRNA";
        802 "sense_intronic";
        860 "transcribed_unprocessed_pseudogene";
       1529 "snoRNA";
       1923 "snRNA";
       2050 "misc_RNA";
       2549 "unprocessed_pseudogene";
       3116 "miRNA";
       9710 "antisense";
      10623 "processed_pseudogene";
      11780 "lincRNA";
      13052 "nonsense_mediated_decay";
      25955 "retained_intron";
      28082 "processed_transcript";

 
But I am not sure from these regions which parts are related to `enhancers`, `promoters`, or `regulatory elements`
