Does fixchr support coord files (from mummer/nucmer)?

[kuangzhuoran]

when set "fixchr -F T", What does this Table file refer to? my command is: "nucmer --mum --mincluster 500 -t 30 $geo1 $geo2 -p XD"

[mnshgl0110]

Sorry for the incomplete documentation. Yes, you can use coords file from fixchr. To generate the suitable coords file from the nucmer output (.delta) file use the following:

show-coords -THrd <input>.delta > <output>.coords

[kuangzhuoran]

Thanks a lot Do delta files need to be filtered?

[mnshgl0110]

It is better to filter out low-quality alignments.

[kuangzhuoran]

thanks a lott