cbc5e17ce713a7076a9f95991e10262079780cc8
max
  Fri May 16 10:27:58 2025 -0700
overload -c to skip internal markers

diff --git src/cbPyLib/cellbrowser/seurat.py src/cbPyLib/cellbrowser/seurat.py
index fcc340c..530b9f4 100644
--- src/cbPyLib/cellbrowser/seurat.py
+++ src/cbPyLib/cellbrowser/seurat.py
@@ -366,31 +366,32 @@
             "convert the data and add the dataset under htmlDir")
 
     parser.add_option("-p", "--port", dest="port", action="store", type="int",
             help="only with --htmlDir: start webserver on port to serve htmlDir")
 
     parser.add_option("-x", "--skipMatrix", dest="skipMatrix", action="store_true",
             default = False,
         help="do not convert the matrix, saves time if the same one has been exported before to the "
         "same outDir directory")
 
     parser.add_option("", "--threads", dest="threadCount", action="store", type="int", default=0,
             help="activate multiprocess strategy, default thread count is 0, which uses no multithreading")
 
     parser.add_option("-m", "--skipMarkers", dest="skipMarkers", action="store_true",
             default = False,
-        help="do not calculate cluster-specific markers with FindAllMarkers(), saves a lot of time")
+        help="do not calculate cluster-specific markers with FindAllMarkers(), saves a lot of time. Also use "
+        "this option if the dataset includes markers in obj@misc and you do not want to use them.")
 
     parser.add_option("-c", "--clusterField", dest="clusterField", action="store",
         help="Cluster field to color on, by default this is the @ident slot of the Seurat object but it can also be any other meta data field of the @meta.data slot")
 
     parser.add_option("", "--markerFile", dest="markerFile", action="store",
             help="Instead of calculating cluster markers again, use this file. Format: cluster,gene,pVal + any other fields. Or alternatively the native Seurat cluster markers format, as created by write.table")
 
     parser.add_option("", "--useMtx", dest="useMtx", action="store_true",
             help="Write a .mtx.gz file, instead of a tsv.gz file. Necessary for big datasets.")
 
     parser.add_option("-s", "--matrixSlot", dest="matrixSlot", action="store", default="counts,data,scale.data",
             help="Export this slot of the matrix. Can be 'counts', 'scale.data' or 'data'. Default is %default. The first value is the default matrix for coloring the plot.")
 
     parser.add_option("", "--assay", dest="assay", action="store",
             help="Select the Seurat3 assay to export.")