mummerplot fails after modifying delta file headers
Entering edit mode
4.5 years ago
Srw ▴ 60

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 > mummerplot -s large --layout -t postscript

Not Successful:

delta-filter -l 150 -i 95 -u 95 -r > sed -i -e 's/chr/Chr/g' mummerplot -s large --layout -t postscript

Writing filtered delta file out.filter

Reading delta file

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.


mummer sed mummerplot • 1.2k views

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