Usage: bgtf count [options]
Arguments:
Required arguments:
-c [PATH] Cell barcode file
-i [STRING] BAM tag of barcode. Default is CB
-g [STRING] feature name to be counted
-r [PATH] Gene BGTF file
Optional arguments:
-b [PATH] Input BAM file
-B [PATH] output gene annotation to a BAM file if set
-d [PATH] Input BAM directory
-m [PATH] RMSK BGTF file. Mask TE if set
-t [INT] n parallel thread if setted
-T [INT] n alignment to process in one thread. Default is 1000000
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