what should I do after mapping the short contigs to cluster?
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utpala101 commented
I want to run the [shortCtgs_to_cluster.pl] to map some short contigs to my cluster, because I got not enough chromosome length (only accounting for 72.02% of total contig length). After running the [shortCtgs_to_cluster.pl], I got the file [shortCtgs.mapped.to.clusters.list]. However, I don't know what to do next, like merging the [list] file to the [summary.cluster] file and then get a new [agp] file?