wgac

create an empty directory

git clone git@github.com:hsiehphLab/WGAC.git .

create a file: fastawhole.fofn which contains the name (or names) of the assembly to run wgac on. This assembly must (I believe) be soft-masked. Not masked will not work because wgac will consider mobile elements to be seg dups. Hard masked will not work because wgac will not be able to extend seg dups using repeats.

So just run it: ./sbatch_run_wgac.sh

Wait for 8 to 12 hours.

If you see a file, summary.txt and summary.xls, then it completed successfully.
Otherwise see me.

To make plots: make -f makefile_wgac all_plots

This must be run in an X environment.

To clean up intermediate files when you are done: make -f makefile_wgac cleanUp_done

The fields (I think) are the following: 1 chromosome 2 start pos 3 end pos 6 orientation _ (underscore) or - is reverse, + is forward duplicated region: 7 chromosome 8 start pos 9 end pos 10 size of the seg dup measured by $9-$8 11 this is some ID for seg dups. if 2 different lines were the same except have 1,2,3 and 7,8,9 reversed, then they had the same field #11. (Please add to this table as you discover the meaning of columns.) (going through the perl script I believe I have found the meaning for the last 13 columns but I am not positive, MV 08/23/2017) 17 The file containing the NW (global) base-level alignment of the 2 seg dups for the line. 18 length of alignment (includes gaps and Ns) 19 indel_N (not sure what the _N and _S are, I think they are indels that are Ns vs real bases) 20 indel_S (but even if I am right I do not know if this is the number of indels or the number of bases that are indels ) 21 the number of aligned bases not including Ns and gaps. (i.e. matches + mismatches) 22 matched bases 23 mismatched bases 24 transitions 25 transversions 26 similarity (not including indels, perfect agreement is 1.0) 27 similarity (including indels) 28 K_jc (Jaccard score) 29 k_kimura (Kimura score)

see wiki.pdf

also see: https://docs.google.com/document/d/1H_kM-mv3idgwaUmbhDl5qrkIdUL2qmqM9YGKsCoRga0/edit?pli=1&tab=t.0