TIP: This tool complements the tool in the Operate on Genomic Intervals tool set which subtracts the intervals of two queries.

Syntax

This tool subtracts an entire query from another query.

• Any text format is valid.
• If both query formats are tabular, you may restrict the subtraction to specific columns contained in both queries and the resulting query will include only the columns specified.
• The begin column must be less than or equal to the end column. If it is not, begin column is switched with end column.
• If begin column is specified but end column is not, end column will default to begin_column (and vice versa).
• All blank and comment lines are skipped and not included in the resulting query (comment lines are lines beginning with a # character).
• Duplicate lines are eliminated from both queries prior to subtraction. If any duplicate lines were eliminated from the first query, the number is displayed in the resulting history item.

Example

If this is the First query:

chr1            4225    19670
chr10           6       8
chr1            24417   24420
chr6_hla_hap2   0       150
chr2            1       5
chr10           2       10
chr1            30      55
chrY            1       20
chr1            1225979 42287290
chr10           7       8

and this is the Second query:

chr1            4225    19670
chr10           6       8
chr1            24417   24420
chr6_hla_hap2   0       150
chr2            1       5
chr1            30      55
chrY            1       20
chr1            1225979 42287290

Subtracting the Second query from the First query (including all columns) will yield:

chr10           7       8
chr10           2       10

Conversely, subtracting the First query from the Second query (including all columns) will result in an empty dataset.

Subtracting the Second query from the First query (restricting to columns c1 and c2) will yield:

chr10           7
chr10           2