1. What are the differences between Flux Capacitor and Flux Simulator?
2. I specified the .PRO file in Flux Capacitor as below:
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ANNOTATION_FILE some_gtf_file.gtf COUNT_ELEMENTS [SPLICE_JUNCTIONS, INTRONS] ANNOTATION_MAPPING AUTO MAPPING_FILE my_bed_file_for_sample1.bed PROFILE_FILE output_dir STATS_FILE output_dir STDERR_FILE output_dir STDOUT_FILE output_dir READ_DESCRIPTOR STRAND_MATE |
However, when I run flux-capacitor -p par_file.par, the following errors appear:
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My questions are: what should I input for READ_DESCRIPTOR? Also, for COUNT_ELEMENTS, are the only options SPLICE_JUNCTIONS and INTRONS? What are the output files for Flux Capacitor?
3. Will any of the Flux Capacitor output files directly useable in Flux Simulator (in its .PRO file, I guess)?