Understanding the LineUp output format

Output format options
If you run LineUp through the lineup.pl script, then you should have elected for plain text, or MySQL output format. The MySQL data will be in a file called filename.mysql (where 'filename' is your original output filename). The plain text parser creates two files: filename_detail.txt; and filename_overview.txt.

If for some reason you do not have these files, you can parse your output file again using lineup2mysql.pl or lineup2txt.pl
MySQL tables
The MySQL parser will create information for two tables. This can be sent into your MySQL database by entering 
mysql -p database < filename.mysql
The tables have the following format:

Detailed results lists every marker pair for every collinear run identified. The table has the format:
  • c1 reference chromosome
  • c2 compared chromosome
  • marker marker name
  • c1_pos position of the marker on c1
  • c2_pos position of the marker on c2
  • block_id id number for the collinear run (block)
  • id unique id number for every pair listing


Results overview lists summary information for each collinear run. There is only one line for each run.
  • c1 reference chromosome
  • c2 compared chromosome
  • len number of pairs involved in the collinear run
  • sum_square sum of square statistic used for significance calculations
  • c1_s start position of the run on c1
  • c1_e end position of the run on c1
  • c2_s start position of the run on c2
  • c2_e end position of the run on c2
  • sig significance level of the collinear run
  • block_id id number for the collinear run (block). This matches with the block_id in the Detailed Results table
  • id another unique id number for every listing
Plain text tables
The plain text parser will create two tables in two files. The tables have the following format:

Detailed results (filename_detail.txt) lists every marker pair for every collinear run identified. Different runs are separated by a line with several "=" signs, the block id number, and the chromosomes between which the collinear run was identified.

The following lines list the marker names involved in the run, and the position on each chromosome. For example 

========== id: 65756 BETWEEN Chr 4 and Chr 2
                    uaz42     52.5     21.0
                    uaz43     52.5     21.0
                    uaz45     52.5     21.0
                    uaz46     52.5     21.0
                    uaz48     52.5     21.0
                    uaz69     52.5     24.7
lists detailed information for run number 65756, which pairs a region on chromosome 4, with a region on chromosome 2. The six markers involved in the run are listed, with their position on chromosome 4, and 2 respectively (it will always be true that the positions are listed under the relevant chromosome name).

Results overview (filename_overview.txt) lists summary information for each collinear run. There is only one line for each run.
  • c1 reference chromosome
  • c2 compared chromosome
  • # markers number of pairs involved in the collinear run
  • ss sum of square statistic used for significance calculations
  • c1s start position of the run on c1
  • c1e end position of the run on c1
  • c2s start position of the run on c2
  • c2e end position of the run on c2
  • sig significance level of the collinear run
  • id id number for the collinear run (block). This matches with the id in the Detailed Results table