I have a filtered delta file that is making a 12x12 comparison. I am successful when plotting the filtered file but the strongest alignments are not on the diagonal when using the -layout preference. I thought it might be because one of my .fasta files uses "chr" and the other uses "Chr". When I change the header from chr ->Chr everything falls apart. mummer returns an error seem below. Here are my two trials
Successful (but layout not on the diagonal):
delta-filter -l 150 -i 95 -u 95 -r results.delta.fasta > results.filter.delta.fast
mummerplot -s large --layout -t postscript results.filter.delta.fasta
Not Successful:
delta-filter -l 150 -i 95 -u 95 -r results.delta.fasta > results.filter.delta.fast
sed -i -e 's/chr/Chr/g' results.filter.delta.fast
mummerplot -s large --layout -t postscript results.filter.delta.fasta
Writing filtered delta file out.filter
Reading delta file results.filter.delta.fasta
Writing plot files out.fplot, out.rplot
ERROR: No alignment data to plot
sed is obviously changing something fundamental about the file that I'm not able to detect. The headers look fine to me. Any and all help would be greatly appreciated.
Thanks.
