Hello to all,
I used a motif of a transcription factor to scan entire genomes of common model organisms with a position weight matrix ( https://ccg.epfl.ch/pwmtools/ ), and got for an organism 4420 hits, when i tried to cluster these hits with a tool in usegalaxy ( cluster ) it produced 2 hit with options : maxium distance between intervals = 20 , minimum number of intervals = 4 but when i changed the option and entered max distance = 5, minimum number of intervals = 4, it produced 4418. Shouldnt the number of hits with max distance = 5 be included to the option with 20? Am i missing something here? I did that to 12 organisms, its the only one that doesnt make any sense.
Thanks and sorry if i didnt explain it the best way possible.
edit : when clicking on the cluster on the right side of the window of usegalaxy, when clicking on the cluster with option 20/4 it shows display in IGB, in IGV and in ucsc but on the 5/4 option it doesnt give the ucsc option if that makes any difference and also i cannot download it wheras i can on the 20/4 option. Also the not logical outcomes are 0 bytes but it still says 4418 regions , on the other hand the one with 2 regions is 41 bytes
