lastz-alignment-awk

genome sorting and plotting the length alignment from the lastz alignment for the node calculations before you import them for the calculations.

gem install youplot
cat lastzalignment.txt | awk '{ print $10 }' | cut -f 1 -d "-" > length1.txt \ 
              && cat lastzalignment.txt | awk '{ print $10 }' | cut -f 2 -d "-" > \
                                          length2.txt && paste length1.txt length2.txt \ 
                                                    | awk '{ print $2-$1 }' | youplot barplot

cat lastzalignment.txt | awk '{ print $12 }' | cut -f 1 -d "-" > length1.txt \ 
              && cat lastzalignment.txt | awk '{ print $12 }' | cut -f 2 -d "-" > \
                                          length2.txt && paste length1.txt length2.txt \ 
                                                    | awk '{ print $2-$1 }' | youplot barplot

Gaurav
Academic Staff Member
Bioinformatics
Institute for Biochemistry and Biology
University of Potsdam
Potsdam,Germany