Hi I am using a GEO dataset with Chip Seq experiments and it has an uploaded bedgraph file and since I need to use bed files for my analysis, is there a way to convert a bedgrpah to bed , also I don't quite understand the difference between both.
[Bedgraph][1] is BED-like, but puts the score data into the fourth column and often contains headers.

To convert to BED, strip out the headers with `grep` and put in a dummy ID value with `awk`:

    $ grep -Ev '^(browser|track|#)' myData.bedgraph \
        | awk ' \
    ​          BEGIN { OFS = "\t"; } \
              { \
                  print $1, $2, $3, "id-"NR, $4; \ 
              } \
        ' - \
        > myData.bed

The five-column BED data now follow the convention of putting the ID into the fourth column, and the score value into the fifth column.

 [1]: http://genome.ucsc.edu/goldenPath/help/bedgraph.html