Hi, I've been observing some strange behavior when using the netFilter tool. I've run the tool with many sets of nets, with and without the -minSizeQ flag. When I use the flag, the resulting nets fill in many gaps as aligning blocks. In other words, the nets are actually altered by the flag. The higher I set -minSizeQ, the more filled the nets become.
For example, if I take the fr2 nets from the hg18 browser and run: netFilter -minSizeQ=1000 hg18.fr2.net.gz > hg18.fr2.filter.net The resulting nets will show huge blocks of alignment, filling in what were gaps in the original nets. Any help is much appreciated. Thanks! Shoa _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
