Description Of 'Bedrnaelements' Format

Question

[Daniel Standage]

I have a colleague that recently downloaded data from this page. He originally thought it was in BED format, but when things didn't look right he checked again and found that it's listed as 'bedRnaElements' format. Here's what a few lines of the file look like.

chr12   49525109        49525231        chr12:49525109:49525231:-:0.82:1.000000 0       -       20710.0541      2.37e-10        0
chr1    8938656 8938824 chr1:8938656:8938824:-:0.32:1.000000    0       -       9668.5513       2.41e-10        0
chr11   65266509        65266572        chr11:65266509:65266572:+:0.06:1.000000 0       +       7722.2007       2.48e-10        0
chr12   120638902       120638965       chr12:120638902:120638965:-:0.63:1.000000       0       -       5807.4491       3.02e-10        0
chr15   69745106        69745303        chr15:69745106:69745303:+:0.53:1.000000 0       +       5875.4584       2.60e-10        0
chr12   6643635 6643713 chr12:6643635:6643713:+:0.69:1.000000   0       +       5168.1132       2.79e-10        0
chr21   33031936        33032132        chr21:33031936:33032132:+:0.26:1.000000 0       +       5458.9421       2.62e-10        0
chr19   36139129        36139287        chr19:36139129:36139287:+:0.12:0.999756 0       +       5009.1252       2.71e-10        0
chr15   44084460        44084571        chr15:44084460:44084571:+:0.29:1.000000 0       +       5240.4456       2.65e-10        0
chr7    56174130        56174250        chr7:56174130:56174250:-:0.43:1.000000  0       -       5573.5338       2.63e-10        0
chr21   35288028        35288174        chr21:35288028:35288174:-:0.02:1.000000 0       -       4141.3189       2.94e-10        0

We have been unable to find a description of the 'bedRnaElements' format so that we can convert the data into something widely usable, such as GFF3, GTF, or BED. Any suggestions?

[Daniel Standage]

Having line wrap for code blocks, by the way, is a horrible idea. Definitely makes this example look a lot messier than it is.

Answer 1

[shuomou]

please see schema here.

http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=expression&hgta_track=wgEncodeCshlShortRnaSeq&hgta_table=wgEncodeCshlShortRnaSeqHpcplCellTapContigs&hgta_doSchema=describe+table+schema