I am trying to use bedtools subtract in the following way:
$ bedtools subtract -a A.bed -b B.bed
but I get the following error:
ERROR: file A.bed has non positional records, which are only valid for the groupBy tool
When I tried to Google the answer, none of the solutions provided seemed to help. Here is the head of A.bed:
$ head A.bed chr1 1 249250621 chr2 1 243199373 chr3 1 198022430 chr4 1 191154276 chr5 1 180915260 chr6 1 171115067 chr7 1 159138663 chrX 1 155270560 chr8 1 146364022 chr9 1 141213431
The cross checked that the columns are tab delimited and the three important columns are in the right order. Additionally, there are no invisible characters after the final column that might throw off Bedtools.
Any insight into the problem would be greatly appreciated!