I am doing an experiment and I need to build a BED12 file for some UTR sequences that I have. I have done a blast for those sequences and with that I was able to build a successful BED6 file, like this:
19 20752377 20758767 ENSDARG00000062634_Kat2b_Tscan 0 +
15 20463447 20464774 ENSDARG00000002336_Dlc_seq01 0 –
However, the script I will use needs the information in the 11th and 12th fields of the BED12. So, I need to go from these UTR sequences to a BED12 file describing them.
My first approach was to look for these UTR coordinates (chrm, start, end) in the UCSC table broweser and download a BED12 file for these coordinates. However, I cannot get a BED12 file that is limited to the coordinates I used as input. It returns me the information for the whole gene/isoform or, if I limit it to the UTR, I cannot get all the fields I need.
chr19 20724346 20755146 ENSDART00000090757.4 0 + 20724453 20752377 0 18 308,139,146,87,182,192,98,126,140,209,127,111,144,115,31,64,85,2963, 0,2755,3093,6826,7286,10788,11063,11242,14594,15533,17592,17815,19837,20058,21142,25091,25257,27837,
Does anyone have any suggestion on how to address this? I need this file to move on with my analysys but I am stuck here for a while now.
Thank you so much!