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Comment: Migrated to Confluence 5.3

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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Code Block
                [ERROR] Read Descriptor {ID}/{STRAND}[0,1,2]/{MATE}[1,2] incompatible with read IDs
java.lang.RuntimeException: Read Descriptor {ID}/{STRAND}[0,1,2]/{MATE}[1,2] incompatible with read IDs
        at barna.flux.capacitor.reconstruction.FluxCapacitor.fileStats(FluxCapacitor.java:2847)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1798)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74)
        at barna.commons.launcher.Flux.main(Flux.java:198)

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)?