Stephen Williams - 2017-04-27

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:

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. Any and all help would be greatly appreciated.

Thanks.