a.bed
looks like this:
chr1 631977 631979 -2.777777778
chr1 631994 631996 31.5625
......
b.bed
looks like this:
chr1 11873 11874 DDX11L1 0 +
chr1 17435 17436 MIR6859-3 0 -
......
After I ran:
closestBed -a a.bed -b b.bed -D b > c.bed
c.bed
looks like this:
chr1 631977 631979 -2.777777778 . -1 -1 . -1 . -1
chr1 631994 631996 31.5625 . -1 -1 . -1 . -1
......
Both a & b were formatted using galaxy before running. Help!
Thanks guys. The spaces were inappropriately added by awk:
There were no spaces in
b.txt
. Any suggestion?Can we have a snapshot of the
b.txt
file? You can edit your answer and add it there.No commas in awk (your script puts spaces (comma) and tabs but you need only tabs: