I have a very basic question about bedtools and bedops. Can I use these tools to filter all the regions where the score is higher (or lower) than a given value?
For example, let's say that I have a BED file like the following:
chr7 127471196 127472363 Pos1 12 + 127471196 127472363 255,0,0
chr7 127472363 127473530 Pos2 200 + 127472363 127473530 255,0,0
chr7 127473530 127474697 Pos3 120 + 127473530 127474697 255,0,0
chr7 127474697 127475864 Pos4 54 + 127474697 127475864 255,0,0
chr7 127475864 127477031 Neg1 2 - 127475864 127477031 0,0,255
chr7 127477031 127478198 Neg2 15 - 127477031 127478198 0,0,255
chr7 127478198 127479365 Neg3 25 - 127478198 127479365 0,0,255
chr7 127479365 127480532 Pos5 2 + 127479365 127480532 255,0,0
chr7 127480532 127481699 Neg4 9 - 127480532 127481699 0,0,255
According to the BED format's specs, the fifth column contains a score, between 0 and 1000 (alternatively, in the bedGraph format the score is on the 4th position). If I want to get all the regions that have a score higher than 20, for example, I can do an awk search:
$: awk '$5 > 20 {print}' mybedfile.bed
However, in order to use awk, I have to keep the BED file in a uncompressed format. It would be much better if I could use the .starch format in Bedops, or if I could combine any Bedops/Bedtools operation with the score search (e.g. get all scores that overlap a region and are higher than a value).
