Closed LQHHHHH closed 5 years ago
Hi. Thanks for using clust and for your question.
Clust aims at extracting tight and optimum clusters without trying to force input genes to be included in the output. It might make sense to get 10,000 genes out of the 40,000+ genes in total, as forcing the rest to be in some clusters would be considered as adding noise to the clusters. However, you may still like to widen your clusters beyond what -t=0.1 gives. Probably try increasing the -q3s parameter to 3.0 for example (default is 2.0), or try to reduce -t to 0.0 (its absolute allowed minimum value).
Please let me know if any more help is needed.
Best Basel
Hi, I am using clust to analyze my two datasets from same species, but I found that only 6,000 genes were clustered and the rest of the genes were not included (40,000+ genes in total), I tried adjusting the -t option. When t=0.1, only 10,000+ genes were clustered. The following is part of my Summary.tsv file contents when t=1.
Do you have any suggestion to increase gene number in clusters, many thanks.